{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T18:47:34Z","timestamp":1788979654180,"version":"build-2803163510"},"reference-count":137,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"the Postdoctoral Fellowship Program of CPSF","award":["No. GZC20241945"],"award-info":[{"award-number":["No. GZC20241945"]}]},{"DOI":"10.13039\/100020760","name":"Sanya Yazhou Bay Science and Technology City","doi-asserted-by":"publisher","award":["No. SYND-2022-04"],"award-info":[{"award-number":["No. SYND-2022-04"]}],"id":[{"id":"10.13039\/100020760","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Expert Workstation in Zhaotong, Yunnan","award":["No. 2021ZTYX05"],"award-info":[{"award-number":["No. 2021ZTYX05"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No. 31922012"],"award-info":[{"award-number":["No. 31922012"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Pests and Diseases Green Prevention and Control Major Special Project","award":["No. 110202201018[LS-02]"],"award-info":[{"award-number":["No. 110202201018[LS-02]"]}]},{"name":"the 2115 Talent Development Program of China Agricultural University"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"DOI":"10.1186\/s12915-025-02429-y","type":"journal-article","created":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T08:26:55Z","timestamp":1761121615000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Hemipteran insects experience recurrent and synergistic molecular evolution adapting to diet shift"],"prefix":"10.1186","volume":"23","author":[{"given":"Ling","family":"Ma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuange","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fanding","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyu","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyou","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shangyuan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanzhi","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8590-1753","authenticated-orcid":false,"given":"Hu","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,22]]},"reference":[{"key":"2429_CR1","doi-asserted-by":"crossref","unstructured":"Abbas A, Dara MZN, Ullah F, Saddam B, Abbas S, Alam A, Babar M, Hafeez F, Gogi MD, Ghramh HA, et al. Unraveling insect feeding patterns and their ecological impacts on plant defense mechanisms. J Plant Dis Prot. 2025;132(1):21.","DOI":"10.1007\/s41348-024-01002-z"},{"key":"2429_CR2","doi-asserted-by":"crossref","unstructured":"McKennaa DD, Shina S, Ahrens I, Balke M, Beza-Beza C, Clarkea DJ, Donathe A, Escalonae HE, Friedrich F, Letsch H, et al. The evolution and genomic basis of beetle diversity. Proc Natl Acad Sci U S A. 2019;116(49):24729\u201337.","DOI":"10.1073\/pnas.1909655116"},{"issue":"6210","key":"2429_CR3","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1126\/science.1257570","volume":"346","author":"B Misof","year":"2014","unstructured":"Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, et al. Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014;346(6210):763\u20137.","journal-title":"Science"},{"key":"2429_CR4","doi-asserted-by":"crossref","unstructured":"Cohen AC. Plant feeding by predatory Heteroptera: evolutionary and adaptational aspects of trophic switching. In: Zoophytophagous Heteroptera: implications for life history and integrated pest management. Lanham: Entomological Society of America; 1996. p. 1\u201317.","DOI":"10.4182\/VKQM1275.1996.1"},{"issue":"5","key":"2429_CR5","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1093\/aesa\/72.5.575","volume":"72","author":"MH Sweet","year":"1979","unstructured":"Sweet MH. On the original feeding habits of the Hemiptera (Insecta). Ann Entomol Soc Am. 1979;72(5):575\u20139.","journal-title":"Ann Entomol Soc Am"},{"key":"2429_CR6","unstructured":"Cobben RH. Evolutionary trends in Heteroptera. Part II. Mouthpart-structures and feeding strategies. Wageningen: Veenman; 1978. p. 5\u2013407."},{"key":"2429_CR7","unstructured":"Schuh RT, Slater JA. True bugs of the world (Hemiptera: Heteroptera): classification and natural history. Ithaca: Cornell University Press; 1995."},{"key":"2429_CR8","volume-title":"True bugs of the world (Hemiptera: Heteroptera): classification and natural history, second eidtion","author":"RT Schuh","year":"2020","unstructured":"Schuh RT, Weirauch C. True bugs of the world (Hemiptera: Heteroptera): classification and natural history, second eidtion. Rochdale, UK: Siri Scientific Press; 2020."},{"issue":"284","key":"2429_CR9","first-page":"20171223","volume":"2017","author":"H Li","year":"1862","unstructured":"Li H, John M, Leavengood J, Chapman EG, Burkhardt D, Song F, et al. Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs. Proc Bio Sci. 1862;2017(284):20171223.","journal-title":"Proc Bio Sci"},{"issue":"1","key":"2429_CR10","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1111\/cla.12233","volume":"35","author":"C Weirauch","year":"2019","unstructured":"Weirauch C, Schuh RT, Cassis G, Wheeler WC. Revisiting habitat and lifestyle transitions in Heteroptera (Insecta: Hemiptera): insights from a combined morphological and molecular phylogeny. Cladistics. 2019;35(1):67\u2013105.","journal-title":"Cladistics"},{"issue":"4","key":"2429_CR11","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1111\/cla.12501","volume":"38","author":"F Ye","year":"2022","unstructured":"Ye F, Kment P, R\u00e9dei D, Luo JY, Wang YH, Kuechler SM, et al. Diversification of the phytophagous lineages of true bugs (Insecta: Hemiptera: Heteroptera) shortly after that of the flowering plants. Cladistics. 2022;38(4):403\u201328.","journal-title":"Cladistics"},{"key":"2429_CR12","doi-asserted-by":"crossref","unstructured":"De Clercq P. Predaceous stinkbugs (Pentatomidae: Asopinae). In: Heteroptera of economic importance. Boca Raton: CRC Press; 2000. p. 759\u2013812.","DOI":"10.1201\/9781420041859-34"},{"issue":"4","key":"2429_CR13","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1111\/syen.12357","volume":"44","author":"YQ Liu","year":"2019","unstructured":"Liu YQ, Li H, Song F, Zhao YS, Wilson JJ, Cai WZ. Higher-level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences. Syst Entomol. 2019;44(4):810\u20139.","journal-title":"Syst Entomol"},{"issue":"2","key":"2429_CR14","doi-asserted-by":"publisher","first-page":"43","DOI":"10.3390\/toxins8020043","volume":"8","author":"AA Walker","year":"2016","unstructured":"Walker AA, Weirauch C, Fry BG, King GF. Venoms of heteropteran insects: a treasure trove of diverse pharmacological toolkits. Toxins. 2016;8(2):43.","journal-title":"Toxins"},{"key":"2429_CR15","doi-asserted-by":"crossref","unstructured":"Krinsky WL. True bugs (Hemiptera). In: Mullen GR, Durden LA, editors. Medical and veterinary entomology. 3rd ed. London: Academic Press; 2019. p.107\u201327.","DOI":"10.1016\/B978-0-12-814043-7.00008-X"},{"issue":"50","key":"2429_CR16","doi-asserted-by":"publisher","first-page":"12775","DOI":"10.1073\/pnas.1815820115","volume":"115","author":"KP Johnson","year":"2018","unstructured":"Johnson KP, Dietrich CH, Friedrich F, Beutel RG, Wipfler B, Peters RS, et al. Phylogenomics and the evolution of hemipteroid insects. Proc Natl Acad Sci U S A. 2018;115(50):12775\u201380.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2429_CR17","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1186\/s12915-024-01991-1","volume":"22","author":"N Song","year":"2024","unstructured":"Song N, Wang MM, Huang WC, Wu ZY, Shao RF, Yin XM. Phylogeny and evolution of hemipteran insects based on expanded genomic and transcriptomic data. BMC Biol. 2024;22(1):190.","journal-title":"BMC Biol"},{"key":"2429_CR18","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2022.104873","author":"YY Cong","year":"2022","unstructured":"Cong YY, Ye XH, Mei Y, He K, Li F. Transposons and non-coding regions drive the intrafamily differences of genome size in insects. iScience. 2022. https:\/\/doi.org\/10.1016\/j.isci.2022.104873.","journal-title":"iScience"},{"issue":"6643","key":"2429_CR19","doi-asserted-by":"publisher","first-page":"1430","DOI":"10.1126\/science.abn1430","volume":"380","author":"AB Osmanski","year":"2023","unstructured":"Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KA, et al. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science. 2023;380(6643):1430.","journal-title":"Science"},{"key":"2429_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13071-017-2005-z","volume":"10","author":"PB Santiago","year":"2017","unstructured":"Santiago PB, de Ara\u00fajo CN, Motta FN, Pra\u00e7a YR, Charneau S, Bastos IMD, et al. Proteases of haematophagous arthropod vectors are involved in blood-feeding, yolk formation and immunity-a review. Parasit Vectors. 2017;10:1\u201320.","journal-title":"Parasit Vectors"},{"key":"2429_CR21","doi-asserted-by":"crossref","unstructured":"Bakke AM, Glover C, Krogdahl \u00c5. 2 - Feeding, digestion and absorption of nutrients. In: Grosell M, Farrell AP, Brauner CJ, editors. Fish physiology: the multifunctional gut of fish. Vol. 30. San Diego: Academic Press; 2010. p. 57\u2013110.","DOI":"10.1016\/S1546-5098(10)03002-5"},{"issue":"2","key":"2429_CR22","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1111\/imb.12151","volume":"24","author":"C Ferreira","year":"2015","unstructured":"Ferreira C, Rebola K, Cardoso C, Bragatto I, Ribeiro AdF, Terra WR. Insect midgut carboxypeptidases with emphasis on S10 hemipteran and M14 lepidopteran carboxypeptidases. Insect Mol Biol. 2015;24(2):222\u201339.","journal-title":"Insect Mol Biol"},{"issue":"2","key":"2429_CR23","first-page":"123","volume":"157","author":"J Lazarevi\u0107","year":"2015","unstructured":"Lazarevi\u0107 J. Jankovi\u0107-Tomani\u0107 MJEEeA. Dietary and phylogenetic correlates of digestive trypsin activity in insect pests. 2015;157(2):123\u201351.","journal-title":"Dietary and phylogenetic correlates of digestive trypsin activity in insect pests"},{"issue":"2","key":"2429_CR24","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1002\/arch.20324","volume":"72","author":"Y Liu","year":"2009","unstructured":"Liu Y, Sui YP, Wang JX, Zhao XF. Characterization of the trypsin-like protease (Ha-TLP2) constitutively expressed in the integument of the cotton bollworm, Helicoverpa armigera. Arch Insect Biochem Physiol. 2009;72(2):74\u201387.","journal-title":"Arch Insect Biochem Physiol"},{"issue":"1","key":"2429_CR25","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s12864-022-08299-w","volume":"23","author":"XF Tang","year":"2022","unstructured":"Tang XF, Huang YH, Li HS, Chen PT, Yang HY, Liang YS, et al. Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). BMC Genomics. 2022;23(1):90.","journal-title":"BMC Genomics"},{"issue":"7","key":"2429_CR26","doi-asserted-by":"publisher","first-page":"2423","DOI":"10.1111\/1755-0998.13434","volume":"21","author":"HJ Huang","year":"2021","unstructured":"Huang HJ, Ye YX, Ye ZX, Yan XT, Wang X, Wei ZY, et al. Chromosome-level genome assembly of the bean bug Riptortus pedestris. Mol Ecol Resour. 2021;21(7):2423\u201336.","journal-title":"Mol Ecol Resour"},{"issue":"1","key":"2429_CR27","doi-asserted-by":"publisher","first-page":"3765","DOI":"10.1038\/ncomms4765","volume":"5","author":"KW Sanggaard","year":"2014","unstructured":"Sanggaard KW, Bechsgaard JS, Fang XD, Duan JJ, Dyrlund TF, Gupta V, et al. Spider genomes provide insight into composition and evolution of venom and silk. Nat Commun. 2014;5(1):3765.","journal-title":"Nat Commun"},{"issue":"11","key":"2429_CR28","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1038\/nrg3483","volume":"14","author":"DL Stern","year":"2013","unstructured":"Stern DL. The genetic causes of convergent evolution. Nat Rev Genet. 2013;14(11):751\u201364.","journal-title":"Nat Rev Genet"},{"issue":"1","key":"2429_CR29","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.tree.2007.09.011","volume":"23","author":"J Arendt","year":"2008","unstructured":"Arendt J, Reznick D. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends Ecol Evol. 2008;23(1):26\u201332.","journal-title":"Trends Ecol Evol"},{"issue":"1","key":"2429_CR30","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1038\/s41467-018-03667-1","volume":"9","author":"V Sharma","year":"2018","unstructured":"Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, Hiller M. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun. 2018;9(1):1215.","journal-title":"Nat Commun"},{"issue":"6435","key":"2429_CR31","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1126\/science.aat7244","volume":"364","author":"TB Sackton","year":"2019","unstructured":"Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, et al. Convergent regulatory evolution and loss of flight in paleognathous birds. Science. 2019;364(6435):74\u20138.","journal-title":"Science"},{"issue":"10","key":"2429_CR32","doi-asserted-by":"publisher","first-page":"2777","DOI":"10.1093\/molbev\/msaa133","volume":"37","author":"G Zancolli","year":"2020","unstructured":"Zancolli G, Casewell NR. Venom systems as models for studying the origin and regulation of evolutionary novelties. Mol Biol Evol. 2020;37(10):2777\u201390.","journal-title":"Mol Biol Evol"},{"issue":"1749","key":"2429_CR33","first-page":"5039","volume":"279","author":"GL Conte","year":"2012","unstructured":"Conte GL, Arnegard ME, Peichel CL, Schluter D. The probability of genetic parallelism and convergence in natural populations. Proc Biol Sci. 2012;279(1749):5039\u201347.","journal-title":"Proc Biol Sci"},{"key":"2429_CR34","doi-asserted-by":"crossref","unstructured":"Manceau M, Domingues VS, Linnen CR, Rosenblum EB, Hoekstra HE. Convergence in pigmentation at multiple levels: mutations, genes and function. Philos Trans R Soc B: Biol Sci. 2010;365(1552):2439\u201350.","DOI":"10.1098\/rstb.2010.0104"},{"issue":"1540","key":"2429_CR35","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1098\/rstb.2009.0263","volume":"365","author":"AP Moczek","year":"2010","unstructured":"Moczek AP. Phenotypic plasticity and diversity in insects. Philos Trans R Soc Lond B Biol Sci. 2010;365(1540):593\u2013603.","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1","key":"2429_CR36","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1007\/s10340-022-01510-7","volume":"96","author":"S Hannigan","year":"2023","unstructured":"Hannigan S, Nendel C, Krull M. Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius. J Pest Sci. 2023;96(1):389\u2013402.","journal-title":"J Pest Sci"},{"issue":"1","key":"2429_CR37","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/s12915-025-02174-2","volume":"23","author":"YH Huang","year":"2025","unstructured":"Huang YH, Escalona HE, Sun Y-F, Zhang PF, Du XY, Gong SR, et al. Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory. BMC Biol. 2025;23(1):67.","journal-title":"BMC Biol"},{"issue":"6","key":"2429_CR38","doi-asserted-by":"publisher","DOI":"10.1093\/gpbjnl\/qzae074","volume":"22","author":"ZY Du","year":"2024","unstructured":"Du ZY, Wang X, Duan YG, Liu SL, Tian L, Song F, et al. Global invasion history and genomic signatures of adaptation of the highly invasive sycamore lace bug. Genomics Proteomics Bioinformatics. 2024;22(6):qzae074.","journal-title":"Genomics Proteomics Bioinformatics"},{"issue":"11","key":"2429_CR39","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20112728","volume":"20","author":"YQ Zhang","year":"2019","unstructured":"Zhang YQ, Li H, Du J, Zhang JZ, Shen J, Cai WZ. Three melanin pathway genes, TH, yellow, and aaNAT, regulate pigmentation in the twin-spotted assassin bug, Platymeris biguttatus (Linnaeus). Int J Mol Sci. 2019;20(11):2728.","journal-title":"Int J Mol Sci"},{"issue":"6","key":"2429_CR40","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","volume":"27","author":"G Marcais","year":"2011","unstructured":"Marcais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27(6):764\u201370.","journal-title":"Bioinformatics"},{"issue":"14","key":"2429_CR41","doi-asserted-by":"publisher","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","volume":"33","author":"GW Vurture","year":"2017","unstructured":"Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017;33(14):2202\u20134.","journal-title":"Bioinformatics"},{"issue":"2","key":"2429_CR42","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"HY Cheng","year":"2021","unstructured":"Cheng HY, Concepcion GT, Feng XW, Zhang HW, Li H. Haplotype-resolved de novo assembly with phased assembly graphs. Nat Methods. 2021;18(2):170\u20135.","journal-title":"Nat Methods"},{"issue":"9","key":"2429_CR43","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","volume":"36","author":"DF Guan","year":"2020","unstructured":"Guan DF, McCarthy SA, Wood J, Howe K, Wang YD, Durbin R. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896\u20138.","journal-title":"Bioinformatics"},{"issue":"14","key":"2429_CR44","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"1","key":"2429_CR45","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016;3(1):95\u20138.","journal-title":"Cell Syst"},{"issue":"6333","key":"2429_CR46","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356(6333):92\u20135.","journal-title":"Science"},{"issue":"1","key":"2429_CR47","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","volume":"21","author":"A Rhie","year":"2020","unstructured":"Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1):245.","journal-title":"Genome Biol"},{"issue":"10","key":"2429_CR48","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-019-0193-0","volume":"12","author":"S Ou","year":"2019","unstructured":"Ou S, Jiang N. Ltr_finder_parallel: parallelization of ltr_finder enabling rapid identification of long terminal repeat retrotransposons. Mob DNA. 2019;12(10):48.","journal-title":"Mob DNA"},{"issue":"18","key":"2429_CR49","first-page":"1","volume":"9","author":"D Ellinghaus","year":"2008","unstructured":"Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9(18):1\u201314.","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"2429_CR50","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1104\/pp.17.01310","volume":"176","author":"S Ou","year":"2017","unstructured":"Ou S, Jiang N. Ltr_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol. 2017;176(2):1410\u201322.","journal-title":"Plant Physiol"},{"issue":"3","key":"2429_CR51","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.molp.2019.02.008","volume":"12","author":"WJ Su","year":"2019","unstructured":"Su WJ, Gu X, Peterson T. TIR-learner, a new ensemble method for TIR transposable element annotation, provides evidence for abundant new transposable elements in the maize genome. Mol Plant. 2019;12(3):447\u201360.","journal-title":"Mol Plant"},{"issue":"28","key":"2429_CR52","doi-asserted-by":"publisher","first-page":"10263","DOI":"10.1073\/pnas.1410068111","volume":"111","author":"WW Xiong","year":"2014","unstructured":"Xiong WW, He LM, Lai JS, Dooner HK, Du CG. Helitronscanner uncovers a large overlooked cache of Helitron transposons in many plant genomes. Proc Natl Acad Sci U S A. 2014;111(28):10263\u20138.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2429_CR53","unstructured":"Smith A, Hubley R, Green P. RepeatMasker open-4.0. 2013."},{"issue":"1\u20134","key":"2429_CR54","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1159\/000084979","volume":"110","author":"J Jurka","year":"2005","unstructured":"Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1\u20134):462\u20137.","journal-title":"Cytogenet Genome Res"},{"issue":"2","key":"2429_CR55","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benso","year":"1999","unstructured":"Benso G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573\u201380.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2429_CR56","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","volume":"12","author":"D Kim","year":"2015","unstructured":"Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357\u201360.","journal-title":"Nat Methods"},{"issue":"3","key":"2429_CR57","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","volume":"33","author":"M Pertea","year":"2015","unstructured":"Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. Stringtie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290\u20135.","journal-title":"Nat Biotechnol"},{"key":"2429_CR58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-6-31","volume":"6","author":"GSC Slater","year":"2005","unstructured":"Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005;6:1\u201311.","journal-title":"BMC Bioinformatics"},{"key":"2429_CR59","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1093\/nar\/gkl200","volume":"34","author":"M Stanke","year":"2006","unstructured":"Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34:435\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2429_CR60","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1101\/gr.6743907","volume":"18","author":"BL Cantarel","year":"2008","unstructured":"Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18(1):188\u201396.","journal-title":"Genome Res"},{"issue":"12","key":"2429_CR61","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. EggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825\u20139.","journal-title":"Mol Biol Evol"},{"issue":"9","key":"2429_CR62","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","volume":"30","author":"P Jones","year":"2014","unstructured":"Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. Interproscan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236\u201340.","journal-title":"Bioinformatics"},{"issue":"15","key":"2429_CR63","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10(15):421\u20139.","journal-title":"BMC Bioinformatics"},{"key":"2429_CR64","doi-asserted-by":"publisher","first-page":"W29","DOI":"10.1093\/nar\/gkr367","volume":"39","author":"RD Finn","year":"2011","unstructured":"Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39:W29-37.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2429_CR65","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772\u201380.","journal-title":"Mol Biol Evol"},{"issue":"15","key":"2429_CR66","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","unstructured":"Capella-Guti\u00e9rrez S, Silla-Mart\u00ednez JM, Gabald\u00f3n T. Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972\u20133.","journal-title":"Bioinformatics"},{"key":"2429_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12983-014-0081-x","volume":"11","author":"P K\u00fcck","year":"2014","unstructured":"K\u00fcck P, Longo GC. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front Zool. 2014;11:1\u20138.","journal-title":"Front Zool"},{"issue":"1","key":"2429_CR68","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.ympev.2013.09.011","volume":"70","author":"P K\u00fcck","year":"2014","unstructured":"K\u00fcck P, Struck TH. Bacola\u2013a heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions. Mol Phylogenet Evol. 2014;70(1):94\u20138.","journal-title":"Mol Phylogenet Evol"},{"issue":"1","key":"2429_CR69","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"LT Nguyen","year":"2015","unstructured":"Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268\u201374.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2429_CR70","doi-asserted-by":"publisher","first-page":"38939","DOI":"10.1038\/srep38939","volume":"6","author":"YH Wang","year":"2016","unstructured":"Wang YH, Engel MS, Rafael JA, Wu HY, R\u00e9dei D, Xie Q, et al. Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda). Sci Rep. 2016;6(1):38939.","journal-title":"Sci Rep"},{"issue":"7475","key":"2429_CR71","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1038\/nature12629","volume":"503","author":"A Nel","year":"2013","unstructured":"Nel A, Roques P, Nel P, Prokin AA, Bourgoin T, Prokop J, et al. The earliest known holometabolous insects. Nature. 2013;503(7475):257\u201361.","journal-title":"Nature"},{"issue":"3","key":"2429_CR72","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1093\/biolinnean\/blx006","volume":"121","author":"K Yoshizawa","year":"2017","unstructured":"Yoshizawa K, Johnson KP, Yao I, Casasola Gonz\u00e1lez JA, Bess E, Aldrete G, et al. Multiple trans-Beringia dispersals of the barklouse genus Trichadenotecnum (Insecta: Psocodea: Psocidae). Biol J Linn Soc. 2017;121(3):501\u201313.","journal-title":"Biol J Linn Soc"},{"key":"2429_CR73","unstructured":"Grimaldi DA, Maisey JG, McCafferty WP, Carle FL, Wighton DC, Popham EJ, Krishna K, Hamilton KGA, Darling DC, Sharkey MJ. Insects from the Santana Formation, Lower Cretaceous, of Brazil. New York: American Museum of Natural History; 1990. p. 1\u2013191."},{"issue":"8","key":"2429_CR74","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586\u201391.","journal-title":"Mol Biol Evol"},{"issue":"10","key":"2429_CR75","doi-asserted-by":"publisher","first-page":"3349","DOI":"10.1534\/g3.117.300233","volume":"7","author":"DR Laetsch","year":"2017","unstructured":"Laetsch DR, Blaxter ML. KinFin: software for taxon-aware analysis of clustered protein sequences. G3. 2017;7(10):3349\u201357.","journal-title":"G3"},{"issue":"1","key":"2429_CR76","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol. 1995;57(1):289\u2013300.","journal-title":"J R Stat Soc Ser B Stat Methodol"},{"key":"2429_CR77","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1146\/annurev-nutr-080508-141048","volume":"30","author":"F Luca","year":"2010","unstructured":"Luca F, Perry G, Di Rienzo A. Evolutionary adaptations to dietary changes. Annu Rev Nutr. 2010;30:291\u2013314.","journal-title":"Annu Rev Nutr"},{"issue":"3","key":"2429_CR78","doi-asserted-by":"publisher","first-page":"1086","DOI":"10.1111\/1755-0998.13516","volume":"22","author":"YL Bai","year":"2022","unstructured":"Bai YL, Shi ZM, Zhou WW, Wang GY, Shi XX, He K, et al. Chromosome-level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem. Mol Ecol Resour. 2022;22(3):1086\u201399.","journal-title":"Mol Ecol Resour"},{"issue":"1","key":"2429_CR79","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1111\/1755-0998.13253","volume":"21","author":"Y Liu","year":"2021","unstructured":"Liu Y, Liu HW, Wang HC, Huang TY, Liu B, Yang B, et al. Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding. Mol Ecol Resour. 2021;21(1):287\u2013300.","journal-title":"Mol Ecol Resour"},{"issue":"1","key":"2429_CR80","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1038\/s41467-018-03091-5","volume":"9","author":"AA Walker","year":"2018","unstructured":"Walker AA, Mayhew ML, Jin J, Herzig V, Undheim EAB, Sombke A, et al. The assassin bug Pristhesancus plagipennis produces two distinct venoms in separate gland lumens. Nat Commun. 2018;9(1):755.","journal-title":"Nat Commun"},{"issue":"10","key":"2429_CR81","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","volume":"22","author":"TD Bie","year":"2006","unstructured":"Bie TD, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics. 2006;22(10):1269\u201371.","journal-title":"Bioinformatics"},{"issue":"W1","key":"2429_CR82","doi-asserted-by":"publisher","first-page":"W317","DOI":"10.1093\/nar\/gkab447","volume":"49","author":"DC Bu","year":"2021","unstructured":"Bu DC, Luo HT, Huo PP, Wang ZH, Zhang S, He ZH, et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res. 2021;49(W1):W317\u201325.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2429_CR83","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15\u201321.","journal-title":"Bioinformatics"},{"issue":"7","key":"2429_CR84","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923\u201330.","journal-title":"Bioinformatics"},{"key":"2429_CR85","doi-asserted-by":"crossref","unstructured":"Zancolli G, Modica MV, Puillandre N, Kantor Y, Barua A, Campli G, Robinson-Rechavi M. Redistribution of ancestral functions underlies the evolution of venom production in marine predatory snails. Mol Biol Evol. 2025;42(5):msaf095.","DOI":"10.1093\/molbev\/msaf095"},{"issue":"2","key":"2429_CR86","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/s41559-023-02281-9","volume":"8","author":"JL Mah","year":"2024","unstructured":"Mah JL, Dunn CW. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nat Ecol Evol. 2024;8(2):325\u201338.","journal-title":"Nat Ecol Evol"},{"key":"2429_CR87","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad106","author":"J Bertram","year":"2023","unstructured":"Bertram J, Fulton B, Tourigny JP, Pe\u00f1a-Garcia Y, Moyle LC, Hahn MW. CAGEE: computational analysis of gene expression evolution. Mol Biol Evol. 2023. https:\/\/doi.org\/10.1093\/molbev\/msad106.","journal-title":"Mol Biol Evol"},{"key":"2429_CR88","doi-asserted-by":"publisher","first-page":"W609","DOI":"10.1093\/nar\/gkl315","volume":"34","author":"M Suyama","year":"2006","unstructured":"Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34:W609\u201312.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2429_CR89","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1093\/molbev\/msv022","volume":"32","author":"MD Smith","year":"2015","unstructured":"Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol. 2015;32(5):1342\u201353.","journal-title":"Mol Biol Evol"},{"key":"2429_CR90","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.16505","volume":"12","author":"LJ Revell","year":"2024","unstructured":"Revell LJ. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ. 2024;12:e16505.","journal-title":"PeerJ"},{"issue":"3","key":"2429_CR91","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","volume":"35","author":"E Paradis","year":"2018","unstructured":"Paradis E, Schliep K. Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2018;35(3):526\u20138.","journal-title":"Bioinformatics"},{"issue":"4","key":"2429_CR92","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.56","volume":"1","author":"SB Xu","year":"2022","unstructured":"Xu SB, Li L, Luo X, Chen MJ, Tang WL, Zhan L, et al. Ggtree: a serialized data object for visualization of a phylogenetic tree and annotation data. iMeta. 2022;1(4):e56.","journal-title":"iMeta"},{"key":"2429_CR93","unstructured":"Ma L. Genome assembly data of Eocanthecona furcellata. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR22405948."},{"key":"2429_CR94","unstructured":"Ma L. Hi-C data of Eocanthecona furcellata. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR22405944."},{"key":"2429_CR95","unstructured":"Ma L. Illumina short-read data of Eocanthecona furcellata. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR22405945."},{"key":"2429_CR96","unstructured":"Ma L. Isoseq data of Eocanthecona furcellata. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR22405946."},{"key":"2429_CR97","unstructured":"Ma L. RNA-seq data of Eocanthecona furcellata. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR22405947."},{"key":"2429_CR98","unstructured":"Ma L. Salivary gland transcriptome data of Eocanthecona furcellata. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/SRR35264038."},{"key":"2429_CR99","unstructured":"Ma L. Genome sequencing raw data of Arma custos. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR27748988."},{"key":"2429_CR100","unstructured":"Ma L. Hi-C raw data of Arma custos. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR27748986."},{"key":"2429_CR101","unstructured":"Ma L. Illumina short-read data of Arma custos. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR27748987."},{"key":"2429_CR102","unstructured":"Ma L. Salivary gland transcriptome data of Arma custos. NCBI Sequence Read Archive. 2025. https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=SRR35264468."},{"key":"2429_CR103","unstructured":"Ma L. Genome assembly of Arma custos. GenBank. 2025. https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/JBEJUF000000000\/."},{"issue":"1","key":"2429_CR104","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1186\/s12864-018-5163-2","volume":"19","author":"D Armisen","year":"2018","unstructured":"Armisen D, Rajakumar R, Friedrich M, Benoit JB, Robertson HM, et al. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water. BMC Genomics. 2018;19(1):832.","journal-title":"BMC Genomics"},{"issue":"1","key":"2429_CR105","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1186\/s12864-021-08249-y","volume":"23","author":"E Bailey","year":"2022","unstructured":"Bailey E, Field L, Rawlings C, King R, Mohareb F, Pak KH, et al. A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics. 2022;23(1):45.","journal-title":"BMC Genomics"},{"issue":"8","key":"2429_CR106","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giz089","volume":"8","author":"Q Liu","year":"2019","unstructured":"Liu Q, Guo Y, Zhang Y, Hu W, Li Y, Zhu D, et al. A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. GigaScience. 2019;8(8):1\u20138.","journal-title":"GigaScience."},{"key":"2429_CR107","doi-asserted-by":"crossref","unstructured":"Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, et al. Brown marmorated stink bug, Halyomorpha halys (St\u00e5l), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics. 2020;21(1):227.","DOI":"10.1186\/s12864-020-6510-7"},{"issue":"1","key":"2429_CR108","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1186\/s13059-019-1660-0","volume":"20","author":"KA Panfilio","year":"2019","unstructured":"Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, et al. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol. 2019;20(1):64.","journal-title":"Genome Biol"},{"issue":"1","key":"2429_CR109","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1111\/1755-0998.13242","volume":"21","author":"WH Ma","year":"2021","unstructured":"Ma WH, Xu L, Hua HX, Chen MJ, Guo MJ, He K, et al. Chromosomal-level genomes of three rice planthoppers provide new insights into sex chromosome evolution. Mol Ecol Resour. 2021;21(1):226\u201337.","journal-title":"Mol Ecol Resour"},{"issue":"9","key":"2429_CR110","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac184","volume":"39","author":"Z Li","year":"2022","unstructured":"Li Z, Li Y, Xue AZ, Dang V, Holmes VR, Johnston JS, et al. The genomic basis of evolutionary novelties in a leafhopper. Mol Biol Evol. 2022;39(9):msac184.","journal-title":"Mol Biol Evol"},{"key":"2429_CR111","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1186\/s12864-015-1525-1","volume":"16","author":"SJ Nicholson","year":"2015","unstructured":"Nicholson SJ, Nickerson ML, Dean M, Song Y, Hoyt PR, Rhee H, et al. The genome of Diuraphis noxia, a global aphid pest of small grains. BMC Genomics. 2015;16:429.","journal-title":"BMC Genomics"},{"issue":"10","key":"2429_CR112","doi-asserted-by":"publisher","first-page":"2143","DOI":"10.1093\/molbev\/msz138","volume":"36","author":"Y Li","year":"2019","unstructured":"Li Y, Park H, Smith TE, Moran NA. Gene family evolution in the pea aphid based on chromosome-level genome assembly. Mol Biol Evol. 2019;36(10):2143\u201356.","journal-title":"Mol Biol Evol"},{"key":"2429_CR113","doi-asserted-by":"crossref","unstructured":"Jiang X, Zhang Q, Qin Y, Yin H, Zhang S, Li Q, et al. A chromosome-level draft genome of the grain aphid Sitobion miscanthi. GigaScience. 2019;8(8):giz101.","DOI":"10.1093\/gigascience\/giz101"},{"key":"2429_CR114","doi-asserted-by":"crossref","unstructured":"Zhao J, Xie L, Zhao X, Li L, Cui J, Chen J. Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae). G3. 2024;14(11):jkae223.","DOI":"10.1093\/g3journal\/jkae223"},{"key":"2429_CR115","doi-asserted-by":"crossref","unstructured":"Chen W, Shakir S, Bigham M, Richter A, Fei Z, Jander G. Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). GigaScience. 2019;8(4):giz033.","DOI":"10.1093\/gigascience\/giz033"},{"issue":"3","key":"2429_CR116","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.1111\/1755-0998.13521","volume":"22","author":"S Zhang","year":"2022","unstructured":"Zhang S, Gao X, Wang L, Jiang W, Su H, Jing T, et al. Chromosome-level genome assemblies of two cotton-melon aphid Aphis gossypii biotypes unveil mechanisms of host adaption. Mol Ecol Resour. 2022;22(3):1120\u201334.","journal-title":"Mol Ecol Resour"},{"issue":"1","key":"2429_CR117","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1111\/1755-0998.13258","volume":"21","author":"R Biello","year":"2021","unstructured":"Biello R, Singh A, Godfrey CJ, Fern\u00e1ndez FF, Mugford ST, Powell G, et al. A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae). Mol Ecol Resour. 2021;21(1):316\u201326.","journal-title":"Mol Ecol Resour"},{"issue":"6","key":"2429_CR118","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1111\/1755-0998.13232","volume":"20","author":"M Li","year":"2020","unstructured":"Li M, Tong H, Wang S, Ye W, Li Z, Omar MAA, et al. A chromosome-level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis. Mol Ecol Resour. 2020;20(6):1733\u201347.","journal-title":"Mol Ecol Resour"},{"issue":"1","key":"2429_CR119","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/s12915-016-0321-y","volume":"14","author":"W Chen","year":"2016","unstructured":"Chen W, Hasegawa DK, Kaur N, Kliot A, Pinheiro PV, Luan J, et al. The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biol. 2016;14(1):110.","journal-title":"BMC Biol"},{"issue":"4","key":"2429_CR120","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1111\/1755-0998.13159","volume":"20","author":"W Xie","year":"2020","unstructured":"Xie W, He C, Fei Z, Zhang Y. Chromosome-level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood). Mol Ecol Resour. 2020;20(4):995\u20131006.","journal-title":"Mol Ecol Resour"},{"issue":"4","key":"2429_CR121","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1111\/1755-0998.13189","volume":"20","author":"SK Guo","year":"2020","unstructured":"Guo SK, Cao LJ, Song W, Shi P, Gao YF, Gong YJ, et al. Chromosome-level assembly of the melon thrips genome yields insights into evolution of a sap-sucking lifestyle and pesticide resistance. Mol Ecol Resour. 2020;20(4):1110\u201325.","journal-title":"Mol Ecol Resour"},{"key":"2429_CR122","doi-asserted-by":"crossref","unstructured":"Ma L, Liu QQ, Wei SJ, Liu SL, Tian L, Song F, et al. Chromosome-level genome assembly of bean flower thrips Megalurothrips usitatus (Thysanoptera: Thripidae). Sci Data. 2023;10(1):252.","DOI":"10.1038\/s41597-023-02164-5"},{"key":"2429_CR123","doi-asserted-by":"crossref","unstructured":"Baldwin-Brown JG, Villa SM, Vickrey AI, Johnson KP, Bush SE, Clayton DH, et al. The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite. G3. 2021;11(2):jkab009.","DOI":"10.1093\/g3journal\/jkab009"},{"key":"2429_CR124","unstructured":"Stillwater O. The whole-genome assembly of Diuraphis noxia. GenBank. 2015. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCF_001186385.1."},{"key":"2429_CR125","unstructured":"Huang Q, Evans JD. The genome assembly of minute pirate bug. GenBank. 2020. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCA_0141190651\/."},{"key":"2429_CR126","unstructured":"Liu Y, Liu H, Wang H, Huang T, Liu B, et al. Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding. GenBank. 2021. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCA_0097395052\/."},{"key":"2429_CR127","unstructured":"Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, et al. Brown marmorated stink bug, Halyomorpha halys (St\u00e5l), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. GenBank. 2020. https:\/\/www.ncbi.nlm.nih.gov\/search\/all\/?term=GCF_0006967952."},{"key":"2429_CR128","unstructured":"Ma WH, Xu L, Hua HX, Chen MJ, Guo MJ, et al. Chromosome-level genome resources of three planthoppers. GenBank. 2021. https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA591478."},{"key":"2429_CR129","unstructured":"Whole genome sequencing of aphid (Aulacorthum solani). GenBank. 2019. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCA_0085288751\/."},{"key":"2429_CR130","unstructured":"Myzus persicae Clone G006 genome assembly and annotation. GenBank. 2017. https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/all\/GCF\/001\/856\/785\/."},{"key":"2429_CR131","unstructured":"Acyrthosiphon pisum genome sequencing and assembly using HiC and Chicago. GenBank. 2019. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCF_0055087852\/."},{"key":"2429_CR132","unstructured":"Diaphorina citri genome assembly Diaci psyllid genome assembly version 1.1. GenBank. 2013. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCF_0004751951\/."},{"key":"2429_CR133","unstructured":"Genome sequencing of Pediculus humanus corporis strain USDA. GenBank. 2007. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCF_0000062951\/."},{"key":"2429_CR134","doi-asserted-by":"crossref","unstructured":"Jiang X, Zhang Q, Qin Y, Yin H, Zhang S,et al. A chromosome-level draft genome of the grain aphid Sitobion miscanthi. GigaScience Database. 2019. http:\/\/gigadb.org\/dataset\/100635.","DOI":"10.1093\/gigascience\/giz101"},{"key":"2429_CR135","doi-asserted-by":"publisher","unstructured":"Liu Q, Guo Y, Zhang Y, Hu W, Li Y, et al. A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. GigaScience. 2019. https:\/\/doi.org\/10.1093\/gigascience\/giz089.","DOI":"10.1093\/gigascience\/giz089"},{"key":"2429_CR136","doi-asserted-by":"crossref","unstructured":"Chen W, Shakir S, Bigham M, Richter A, Fei Z, Jander G. Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). GigaScience Database. 2019. http:\/\/gigadb.org\/dataset\/100572.","DOI":"10.1101\/438499"},{"key":"2429_CR137","doi-asserted-by":"crossref","unstructured":"Ma L. Chromosome-level genome assembly of bean flower thrips Megalurothrips usitatus. Figshare. 2023. https:\/\/doi.org\/106084\/m9figsharec6603697v1.","DOI":"10.1038\/s41597-023-02164-5"}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-025-02429-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-025-02429-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-025-02429-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T09:03:58Z","timestamp":1761123838000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-025-02429-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,22]]},"references-count":137,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["2429"],"URL":"https:\/\/doi.org\/10.1186\/s12915-025-02429-y","relation":{},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,22]]},"assertion":[{"value":"29 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"320"}}