{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T17:40:20Z","timestamp":1778175620533,"version":"3.51.4"},"reference-count":83,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,11,16]],"date-time":"2024-11-16T00:00:00Z","timestamp":1731715200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,11,16]],"date-time":"2024-11-16T00:00:00Z","timestamp":1731715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Science and Technology Innovation Project of Laoshan Laboratory","award":["LSKJ202203100"],"award-info":[{"award-number":["LSKJ202203100"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["41806202"],"award-info":[{"award-number":["41806202"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32201219"],"award-info":[{"award-number":["32201219"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42221005"],"award-info":[{"award-number":["42221005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science Fund Program for Distinguished Young Scholars of Shandong Province","award":["2022HWYQ-087"],"award-info":[{"award-number":["2022HWYQ-087"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"DOI":"10.1186\/s40168-024-01960-4","type":"journal-article","created":{"date-parts":[[2024,11,16]],"date-time":"2024-11-16T03:06:22Z","timestamp":1731726382000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Integrated multi-approaches reveal unique metabolic mechanisms of Vestimentifera to adapt to deep sea"],"prefix":"10.1186","volume":"12","author":[{"given":"Qinglei","family":"Sun","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zihao","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanyuan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,11,16]]},"reference":[{"key":"1960_CR1","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1126\/science.213.4505.336","volume":"213","author":"H Felbeck","year":"1981","unstructured":"Felbeck H. Chemoautotrophic potential of the hydrothermal vent tube worm, Riftia pachyptila Jones (Vestimentifera). Science. 1981;213:336\u20138.","journal-title":"Science"},{"key":"1960_CR2","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/j.ympev.2015.02.008","volume":"85","author":"Y Li","year":"2015","unstructured":"Li Y, Kocot KM, Schander C, Santos SR, Thornhill DJ, Halanych KM. Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida). Mol Phylogenet Evol. 2015;85:221\u20139.","journal-title":"Mol Phylogenet Evol"},{"key":"1960_CR3","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1111\/zsc.12201","volume":"46","author":"Y Li","year":"2017","unstructured":"Li Y, et al. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zool Scr. 2017;46:200\u201313.","journal-title":"Zool Scr"},{"key":"1960_CR4","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1002\/jmor.20677","volume":"278","author":"NN Rimskaya-Korsakova","year":"2017","unstructured":"Rimskaya-Korsakova NN, Galkin SV, Malakhov VV. The anatomy of the blood vascular system of the giant vestimentiferan tubeworm Riftia pachyptila (Siboglinidae, Annelida). J Morphol. 2017;278:810\u201327.","journal-title":"J Morphol"},{"key":"1960_CR5","doi-asserted-by":"publisher","first-page":"3638","DOI":"10.1111\/1462-2920.12427","volume":"16","author":"J Zimmermann","year":"2014","unstructured":"Zimmermann J, et al. Dual symbiosis with co-occurring sulfur-oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent. Environ Microbiol. 2014;16:3638\u201356.","journal-title":"Environ Microbiol"},{"key":"1960_CR6","doi-asserted-by":"publisher","first-page":"4116","DOI":"10.1093\/molbev\/msab203","volume":"38","author":"Y Sun","year":"2021","unstructured":"Sun Y, et al. Genomic signatures supporting the symbiosis and formation of chitinous tube in the deep-sea tubeworm Paraescarpia echinospica. Mol Biol Evol. 2021;38:4116\u201334.","journal-title":"Mol Biol Evol"},{"key":"1960_CR7","doi-asserted-by":"publisher","first-page":"2814","DOI":"10.1038\/s41467-023-38521-6","volume":"14","author":"G Moggioli","year":"2023","unstructured":"Moggioli G, et al. Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms. Nat Commun. 2023;14:2814.","journal-title":"Nat Commun"},{"key":"1960_CR8","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s12864-023-09166-y","volume":"24","author":"M Wang","year":"2023","unstructured":"Wang M, et al. The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment. BMC Genomics. 2023;24:72.","journal-title":"BMC Genomics"},{"key":"1960_CR9","doi-asserted-by":"publisher","first-page":"msab347","DOI":"10.1093\/molbev\/msab347","volume":"9","author":"AL de Oliveira","year":"2022","unstructured":"de Oliveira AL, Mitchell J, Girguis P, Bright M. Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome. Mol Biol Evol. 2022;9:msab347.","journal-title":"Mol Biol Evol"},{"key":"1960_CR10","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s12915-019-0713-x","volume":"17","author":"Y Li","year":"2019","unstructured":"Li Y, Tassia MG, Waits DS, Bogantes VE, David KT, Halanych KM. Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biol. 2019;17:91.","journal-title":"BMC Biol"},{"key":"1960_CR11","doi-asserted-by":"publisher","first-page":"3237","DOI":"10.1111\/j.1462-2920.2008.01712.x","volume":"10","author":"T L\u00f6sekann","year":"2008","unstructured":"L\u00f6sekann T, Robador A, Niemann H, Knittel K, Boetius A, Dubilier N. Endosymbioses between bacteria and deep-sea siboglinid tubeworms from an Arctic cold seep (Haakon Mosby mud volcano, Barents Sea). Environ Microbiol. 2008;10:3237\u201354.","journal-title":"Environ Microbiol"},{"key":"1960_CR12","doi-asserted-by":"publisher","first-page":"260","DOI":"10.2307\/1541878","volume":"173","author":"SC Hand","year":"1987","unstructured":"Hand SC. Trophosome ultrastructure and the characterization of isolated bacteriocytes from invertebrate-sulfur bacteria symbioses. Biol Bull. 1987;173:260\u201376.","journal-title":"Biol Bull"},{"key":"1960_CR13","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1111\/1758-2229.12994","volume":"13","author":"T Zvi-Kedem","year":"2021","unstructured":"Zvi-Kedem T, Shemesh E, Tchernov D, Rubin-Blum M. The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms. Environ Microbiol Rep. 2021;13:744\u201352.","journal-title":"Environ Microbiol Rep"},{"key":"1960_CR14","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41396-019-0520-y","volume":"14","author":"Y Yang","year":"2020","unstructured":"Yang Y, et al. Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts. ISME J. 2020;14:135\u201350.","journal-title":"ISME J"},{"key":"1960_CR15","doi-asserted-by":"publisher","first-page":"2785","DOI":"10.1038\/s41396-018-0220-z","volume":"12","author":"Y Li","year":"2018","unstructured":"Li Y, Liles MR, Halanych KM. Endosymbiont genomes yield clues of tubeworm success. ISME J. 2018;12:2785\u201395.","journal-title":"ISME J"},{"key":"1960_CR16","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s40168-018-0411-x","volume":"6","author":"J Reveillaud","year":"2018","unstructured":"Reveillaud J, Anderson R, Reves-Sohn S, Cavanaugh C, Huber JA. Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity. Microbiome. 2018;6:19.","journal-title":"Microbiome"},{"key":"1960_CR17","doi-asserted-by":"publisher","first-page":"5197","DOI":"10.1128\/AEM.00953-16","volume":"82","author":"M Perez","year":"2016","unstructured":"Perez M, Juniper K. Insights into symbiont population structure among three vestimentiferan tubeworm host species at eastern Pacific spreading centers. Appl Environ Microbiol. 2016;82:5197\u2013205.","journal-title":"Appl Environ Microbiol"},{"key":"1960_CR18","doi-asserted-by":"publisher","first-page":"e00394","DOI":"10.1128\/mSphere.00394-18","volume":"4","author":"M Rubin-Blum","year":"2019","unstructured":"Rubin-Blum M, Dubilier N, Kleiner M. Genetic evidence for two carbon fixation pathways (the Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle) in symbiotic and free-living bacteria. mSphere. 2019;4:e00394-18.","journal-title":"mSphere"},{"key":"1960_CR19","doi-asserted-by":"publisher","first-page":"e02243","DOI":"10.1128\/mBio.02243-19","volume":"10","author":"T Hinzke","year":"2019","unstructured":"Hinzke T, et al. Host-microbe interactions in the chemosynthetic Riftia pachyptila symbiosis. mBio. 2019;10:e02243-19.","journal-title":"mBio"},{"key":"1960_CR20","first-page":"345","volume":"122","author":"M Bright","year":"2005","unstructured":"Bright M, Sorgo A. Ultrastructural reinvestigation of the trophosome in adults of Riftia pachyptila (Annelida, Siboglinidae). Invertebr Biol. 2005;122:345\u201366.","journal-title":"Invertebr Biol"},{"key":"1960_CR21","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1007\/s002270050722","volume":"136","author":"M Bright","year":"2000","unstructured":"Bright M, Keckeism H, Fisher CR. An autoradiographic examination of carbon fixation, transfer and utilization in the Riftia pachyptila symbiosis. Mar Biol. 2000;136:621\u201332.","journal-title":"Mar Biol"},{"key":"1960_CR22","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1086\/515931","volume":"71","author":"H Felbeck","year":"1998","unstructured":"Felbeck H, Jarchow J. Carbon release from purified chemoautotrophic bacterial symbionts of the hydrothermal vent tubeworm Riftia pachyptila. Physiol Zool. 1998;71:294\u2013302.","journal-title":"Physiol Zool"},{"key":"1960_CR23","doi-asserted-by":"publisher","first-page":"687","DOI":"10.3390\/microorganisms8050687","volume":"8","author":"QL Sun","year":"2020","unstructured":"Sun QL, et al. High-throughput sequencing reveals a potentially novel Sulfurovum species dominating the microbial communities of the seawater-sediment interface of a deep-sea cold seep in South China Sea. Microorganisms. 2020;8:687.","journal-title":"Microorganisms"},{"key":"1960_CR24","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen E, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852\u20137.","journal-title":"Nat Biotechnol"},{"key":"1960_CR25","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.micres.2015.05.006","volume":"177","author":"J Zhang","year":"2015","unstructured":"Zhang J, Sun QL, Zeng ZG, Chen S, Sun L. Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge. Okinawa Trough Microbiol Res. 2015;177:43\u201352.","journal-title":"Okinawa Trough Microbiol Res"},{"key":"1960_CR26","doi-asserted-by":"publisher","first-page":"2802","DOI":"10.1128\/aem.63.7.2802-2813.1997","volume":"63","author":"JJ Godon","year":"1997","unstructured":"Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol. 1997;63:2802\u201313.","journal-title":"Appl Environ Microbiol"},{"key":"1960_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix133","volume":"7","author":"C Fang","year":"2018","unstructured":"Fang C, et al. Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing. Gigascience. 2018;7:1\u20138.","journal-title":"Gigascience"},{"key":"1960_CR28","doi-asserted-by":"publisher","first-page":"gix024","DOI":"10.1093\/gigascience\/gix024","volume":"6","author":"J Huang","year":"2017","unstructured":"Huang J, et al. A reference human genome dataset of the BGISEQ-500 sequencer. Gigascience. 2017;6:gix024.","journal-title":"Gigascience"},{"key":"1960_CR29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix120","volume":"7","author":"Y Chen","year":"2018","unstructured":"Chen Y, et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2018;7:1\u20136.","journal-title":"Gigascience"},{"key":"1960_CR30","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/2047-217X-1-18","volume":"1","author":"R Luo","year":"2012","unstructured":"Luo R, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:18.","journal-title":"Gigascience"},{"key":"1960_CR31","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1101\/gr.213959.116","volume":"27","author":"S Nurk","year":"2017","unstructured":"Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824\u201334.","journal-title":"Genome Res"},{"key":"1960_CR32","doi-asserted-by":"publisher","first-page":"e132","DOI":"10.1093\/nar\/gkq275","volume":"38","author":"W Zhu","year":"2010","unstructured":"Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38:e132.","journal-title":"Nucleic Acids Res"},{"key":"1960_CR33","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150\u20132.","journal-title":"Bioinformatics"},{"key":"1960_CR34","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","volume":"6","author":"GV Uritskiy","year":"2018","unstructured":"Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6:158.","journal-title":"Microbiome"},{"key":"1960_CR35","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043\u201355.","journal-title":"Genome Res"},{"key":"1960_CR36","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674\u20136.","journal-title":"Bioinformatics"},{"key":"1960_CR37","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","volume":"34","author":"NL Bray","year":"2016","unstructured":"Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34:525\u20137.","journal-title":"Nat Biotechnol"},{"key":"1960_CR38","doi-asserted-by":"publisher","first-page":"43","DOI":"10.11646\/zootaxa.4294.4.4","volume":"4294","author":"L Verrastro","year":"2017","unstructured":"Verrastro L, Maneyro R, Da Silva CM, Farias I. A new species of lizard of the L wiegmannii group (Iguania: Liolaemidae) from the Uruguayan Savanna. Zootaxa. 2017;4294:43.","journal-title":"Zootaxa"},{"key":"1960_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/sdata.2018.156","volume":"5","author":"P Heller","year":"2018","unstructured":"Heller P, Casaletto J, Ruiz G, Geller J. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Sci Data. 2018;5:1\u20137.","journal-title":"Sci Data"},{"key":"1960_CR40","doi-asserted-by":"publisher","first-page":"giy104","DOI":"10.1093\/gigascience\/giy104","volume":"7","author":"H Liu","year":"2018","unstructured":"Liu H, et al. Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. Gigascience. 2018;7:giy104.","journal-title":"Gigascience"},{"key":"1960_CR41","unstructured":"Liu B, et al. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. arXiv. 2013. https:\/\/arxiv.org\/abs\/1308.2012."},{"key":"1960_CR42","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1038\/nmeth.4035","volume":"13","author":"CS Chin","year":"2016","unstructured":"Chin CS, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature methods. 2016;13:1050\u20134.","journal-title":"Nature methods."},{"key":"1960_CR43","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/nmeth.2474","volume":"10","author":"CS Chin","year":"2013","unstructured":"Chin CS, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10:563.","journal-title":"Nat Methods"},{"key":"1960_CR44","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Sim\u00e3o","year":"2015","unstructured":"Sim\u00e3o FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210\u20132.","journal-title":"Bioinformatics"},{"key":"1960_CR45","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"LR Durbin","year":"2009","unstructured":"Durbin LR. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754\u201360.","journal-title":"Bioinformatics"},{"key":"1960_CR46","first-page":"656","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ. BLAT\u2014the BLAST-like alignment tool. Genome Res. 2002;12:656\u201364.","journal-title":"Genome Res"},{"key":"1960_CR47","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1101\/gr.88502","volume":"12","author":"Z Bao","year":"2002","unstructured":"Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002;12:1269\u201376.","journal-title":"Genome Res"},{"issue":"Suppl 1","key":"1960_CR48","doi-asserted-by":"publisher","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","volume":"21","author":"AL Price","year":"2005","unstructured":"Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(Suppl 1):i351-8.","journal-title":"Bioinformatics"},{"key":"1960_CR49","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","volume":"6","author":"W Bao","year":"2015","unstructured":"Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11.","journal-title":"Mob DNA"},{"key":"1960_CR50","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1741-7007-4-41","volume":"4","author":"EM Gertz","year":"2006","unstructured":"Gertz EM, Yu YK, Agarwala R, Sch\u00e4ffer AA, Altschul SF. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006;4:41.","journal-title":"BMC Biol"},{"key":"1960_CR51","doi-asserted-by":"publisher","first-page":"988","DOI":"10.1101\/gr.1865504","volume":"14","author":"E Birney","year":"2004","unstructured":"Birney E, Clamp M, Durbin R. GeneWise and Genomewise. Genome Res. 2004;14:988\u201395.","journal-title":"Genome Res"},{"key":"1960_CR52","doi-asserted-by":"publisher","first-page":"W465","DOI":"10.1093\/nar\/gki458","volume":"33","author":"S Mario","year":"2005","unstructured":"Mario S, Burkhard M. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005;33:W465\u20137.","journal-title":"Nucleic Acids Res"},{"key":"1960_CR53","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/0022-2836(92)90130-C","volume":"226","author":"R Guig\u00f3","year":"1992","unstructured":"Guig\u00f3 R, Knudsen S, Drake N, Smith T. Prediction of gene structure. J Mol Biol. 1992;226:141\u201357.","journal-title":"J Mol Biol"},{"key":"1960_CR54","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C Burge","year":"1997","unstructured":"Burge C. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78\u201394.","journal-title":"J Mol Biol"},{"key":"1960_CR55","doi-asserted-by":"publisher","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","volume":"20","author":"W Majoros","year":"2004","unstructured":"Majoros W, Pertea M, Salzberg S. TigrScan & GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004;20:2878\u20139.","journal-title":"Bioinformatics"},{"key":"1960_CR56","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/1471-2105-5-59","volume":"5","author":"I Korf","year":"2004","unstructured":"Korf I. Gene finding in novel genomes. BMC bioinformatics. 2004;5:59.","journal-title":"BMC bioinformatics."},{"key":"1960_CR57","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","volume":"29","author":"MG Grabherr","year":"2011","unstructured":"Grabherr MG, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644\u201352.","journal-title":"Nat Biotechnol"},{"key":"1960_CR58","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1038\/nprot.2016.095","volume":"11","author":"M Pertea","year":"2016","unstructured":"Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT. StringTie and Ballgown Nat Protoc. 2016;11:1650\u201367.","journal-title":"StringTie and Ballgown Nat Protoc"},{"key":"1960_CR59","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.","journal-title":"Genome Biol"},{"key":"1960_CR60","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;33:290\u20135.","journal-title":"Nat Biotechnol"},{"key":"1960_CR61","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1038\/nprot.2012.016","volume":"7","author":"C Trapnell","year":"2012","unstructured":"Trapnell C, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562\u201378.","journal-title":"Nat Protoc"},{"key":"1960_CR62","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","volume":"9","author":"BJ Haas","year":"2008","unstructured":"Haas BJ, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9:R7.","journal-title":"Genome Biol"},{"key":"1960_CR63","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114\u201320.","journal-title":"Bioinformatics."},{"key":"1960_CR64","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders S, Pyl PT, Huber W. HTSeq\u2014a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166\u20139.","journal-title":"Bioinformatics"},{"key":"1960_CR65","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.","journal-title":"Genome Biol"},{"issue":"1533\u20131545","key":"1960_CR66","volume":"175","author":"XX Shen","year":"2018","unstructured":"Shen XX, et al. Tempo and mode of genome evolution in the budding yeast subphylum. Cell. 2018;175(1533\u20131545): e20.","journal-title":"Cell"},{"key":"1960_CR67","doi-asserted-by":"publisher","first-page":"E1173","DOI":"10.1073\/pnas.1121198109","volume":"109","author":"M Kleiner","year":"2012","unstructured":"Kleiner M, et al. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci USA. 2012;109:E1173\u201382.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1960_CR68","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/B978-0-12-386905-0.00001-2","volume":"495","author":"VN Khmelenina","year":"2011","unstructured":"Khmelenina VN, Rozova ON, Trotsenko YA. Characterization of the recombinant pyrophosphate-dependent 6-phosphofructokinases from Methylomicrobium alcaliphilum 20z and Methylococcus capsulatus Bath. Method Enzymol. 2011;495:1\u201314.","journal-title":"Method Enzymol"},{"key":"1960_CR69","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/371663a0","volume":"371","author":"R Lutz","year":"1994","unstructured":"Lutz R, et al. Rapid growth at deep-sea vents. Nature. 1994;371:663\u20134.","journal-title":"Nature"},{"key":"1960_CR70","doi-asserted-by":"publisher","first-page":"115","DOI":"10.3354\/meps231115","volume":"231","author":"A Sorgo","year":"2002","unstructured":"Sorgo A, Gaill F, Lechaire JP, Arndt C, Bright M. Glycogen storage in the Riftia pachyptila trophosome: contribution of host and symbionts. Mar Ecol Prog Ser. 2002;231:115\u201320.","journal-title":"Mar Ecol Prog Ser"},{"key":"1960_CR71","doi-asserted-by":"publisher","first-page":"e58371","DOI":"10.7554\/eLife.58371","volume":"10","author":"T Hinzke","year":"2021","unstructured":"Hinzke T, et al. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. Elife. 2021;10:e58371.","journal-title":"Elife"},{"key":"1960_CR72","first-page":"e00754","volume":"6","author":"NJ Shikuma","year":"2021","unstructured":"Shikuma NJ. Bacteria-stimulated metamorphosis: an ocean of insights from investigating a transient host-microbe interaction. Systems. 2021;6:e00754-21.","journal-title":"Systems."},{"key":"1960_CR73","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1080\/19336934.2017.1283081","volume":"11","author":"T Miyamoto","year":"2017","unstructured":"Miyamoto T, Amrein H. Gluconeogenesis: an ancient biochemical pathway with a new twist. Fly (Austin). 2017;11:218\u201323.","journal-title":"Fly (Austin)"},{"key":"1960_CR74","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1074\/jbc.M114.619411","volume":"290","author":"H Matsuda","year":"2015","unstructured":"Matsuda H, Yamada T, Yoshida M, Nishimura T. Flies without trehalose. J Biol Chem. 2015;290:1244\u201355.","journal-title":"J Biol Chem"},{"key":"1960_CR75","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1016\/j.cub.2019.02.053","volume":"29","author":"T Miyamoto","year":"2019","unstructured":"Miyamoto T, Amrein H. Neuronal gluconeogenesis regulates systemic glucose homeostasis in Drosophila melanogaster. Curr Biol. 2019;29:1263-1272.e5.","journal-title":"Curr Biol"},{"key":"1960_CR76","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/S0378-1097(96)00455-7","volume":"146","author":"JC Arguelles","year":"1997","unstructured":"Arguelles JC. Thermotolerance and trehalose accumulation induced by heat shock in yeast cells of Candida albicans. FEMS Microbiol Lett. 1997;146:65\u201371.","journal-title":"FEMS Microbiol Lett"},{"key":"1960_CR77","doi-asserted-by":"publisher","first-page":"3516","DOI":"10.1242\/jeb.02404","volume":"209","author":"PR Girguis","year":"2006","unstructured":"Girguis PR, Childress JJ. Metabolite uptake, stoichiometry and chemoautotrophic function of the hydrothermal vent tubeworm Riftia pachyptila: responses to environmental variations in substrate concentrations and temperature. J Exp Biol. 2006;209:3516\u201328.","journal-title":"J Exp Biol"},{"key":"1960_CR78","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1999-3110-55-20","volume":"55","author":"ZG Li","year":"2014","unstructured":"Li ZG, Luo LJ, Zhu LP. Involvement of trehalose in hydrogen sulfide donor sodium hydrosulfide-induced the acquisition of heat tolerance in maize (Zea mays L) seedlings. Bot Stud. 2014;55:20.","journal-title":"Bot Stud."},{"key":"1960_CR79","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1111\/1744-7917.12650","volume":"27","author":"JX Chen","year":"2020","unstructured":"Chen JX, Lyu ZH, Wang CY, Cheng J, Lin T. RNA interference of a trehalose-6-phosphate synthase gene reveals its roles in the biosynthesis of chitin and lipids in Heortia vitessoides (Lepidoptera: Crambidae). Insect Sci. 2020;27:212\u201323.","journal-title":"Insect Sci"},{"key":"1960_CR80","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/nrg2386","volume":"9","author":"PJ Keeling","year":"2008","unstructured":"Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet. 2008;9:605\u201318.","journal-title":"Nat Rev Genet"},{"key":"1960_CR81","doi-asserted-by":"publisher","first-page":"2370","DOI":"10.1093\/gbe\/evaa208","volume":"12","author":"JD Galbraith","year":"2020","unstructured":"Galbraith JD, Ludington AJ, Suh A, Sanders KL, Adelson DL. New environment, new invaders\u2014repeated horizontal transfer of LINEs to sea snakes. Genome Biol Evol. 2020;12:2370\u201383.","journal-title":"Genome Biol Evol"},{"key":"1960_CR82","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1016\/j.tig.2021.02.006","volume":"37","author":"LA Graham","year":"2021","unstructured":"Graham LA, Davies PL. Horizontal gene transfer in vertebrates: a fishy tale. Trends Genet. 2021;37:501\u20133.","journal-title":"Trends Genet"},{"key":"1960_CR83","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/1471-2148-11-239","volume":"11","author":"C R\u00f6delsperger","year":"2011","unstructured":"R\u00f6delsperger C, Sommer RJ. Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects. BMC Evol Biol. 2011;11:239.","journal-title":"BMC Evol Biol"}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01960-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-024-01960-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01960-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T02:12:22Z","timestamp":1739412742000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-024-01960-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,16]]},"references-count":83,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1960"],"URL":"https:\/\/doi.org\/10.1186\/s40168-024-01960-4","relation":{},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,16]]},"assertion":[{"value":"15 June 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 October 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 November 2024","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":"241"}}