{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T02:19:44Z","timestamp":1784600384290,"version":"3.55.0"},"reference-count":79,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31802273"],"award-info":[{"award-number":["31802273"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005063","name":"Excellent Young Talents Fund Program of Higher Education Institutions of Anhui Province","doi-asserted-by":"publisher","award":["gxyqZD2021097"],"award-info":[{"award-number":["gxyqZD2021097"]}],"id":[{"id":"10.13039\/501100005063","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fishery Industrial System of Anhui Province, China","award":["[2021]711"],"award-info":[{"award-number":["[2021]711"]}]},{"name":"Major Science and Technology Project of Anhui Province","award":["18030701173"],"award-info":[{"award-number":["18030701173"]}]},{"name":"Open Project of State Key Laboratory of Freshwater Ecology and Biotechnology","award":["2016FB16"],"award-info":[{"award-number":["2016FB16"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The turtle carapace is composed of severely deformed fused dorsal vertebrae, ribs, and bone plates. In particular, the lateral growth in the superficial layer of turtle ribs in the dorsal trunk causes an encapsulation of the scapula and pelvis. The recent study suggested that the carapacial ridge (CR) is a new model of epithelial\u2013mesenchymal transition which is essential for the arrangement of the ribs. Therefore, it is necessary to explore the regulatory mechanism of carapacial ridge development to analyze the formation of the turtle shell. However, the current understanding of the regulatory network underlying turtle carapacial ridge development is poor due to the lack of both systematic gene screening at different carapacial ridge development stages and gene function verification studies. In this study, we obtained genome-wide gene transcription and gene translation profiles using RNA sequencing and ribosome nascent-chain complex mRNA sequencing from carapacial ridge tissues of Chinese soft-shell turtle at different development stages. A correlation analysis of the transcriptome and translatome revealed that there were 129, 670, and 135 codifferentially expressed genes, including homodirection and opposite-direction differentially expressed genes, among three comparison groups, respectively. The pathway enrichment analysis of codifferentially expressed genes from the Kyoto Encyclopedia of Genes and Genomes showed dynamic changes in signaling pathways involved in carapacial ridge development. Especially, the results revealed that the Wnt signaling pathway and MAPK signaling pathway may play important roles in turtle carapacial ridge development. In addition, Wnt and Fgf were expressed during the carapacial ridge development. Furthermore, we discovered that Wnt5a regulated carapacial ridge development through the Wnt5a\/JNK pathway. Therefore, our studies uncover that the morphogenesis of the turtle carapace might function through the co-operation between conserved WNT and FGF signaling pathways. Consequently, our findings revealed the dynamic signaling pathways acting on the carapacial ridge development of Chinese soft-shell turtle and provided new insights into uncover the molecular mechanism underlying turtle shell morphogenesis.<\/jats:p>","DOI":"10.3390\/ijms222212441","type":"journal-article","created":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T08:53:56Z","timestamp":1637225636000},"page":"12441","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle"],"prefix":"10.3390","volume":"22","author":[{"given":"Jun","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8754-1736","authenticated-orcid":false,"given":"Peng","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"},{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinyan","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayu","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingtao","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiantian","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuanhe","family":"Bao","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiping","family":"Su","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Fang","family":"Gui","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1002\/jmor.10766","article-title":"Skeletal development in the Chinese soft-shelled turtle Pelodiscus sinensis (Testudines: Trionychidae)","volume":"270","author":"Muller","year":"2009","journal-title":"J. Morphol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1002\/dvdy.20235","article-title":"Turtle-chicken chimera: An experimental approach to understanding evolutionary innovation in the turtle","volume":"232","author":"Nagashima","year":"2005","journal-title":"Dev. Dynam."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.1242\/dev.002618","article-title":"On the carapacial ridge in turtle embryos: Its developmental origin, function and the chelonian body plan","volume":"134","author":"Nagashima","year":"2007","journal-title":"Development"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.gde.2017.03.016","article-title":"Patterning of the turtle shell","volume":"45","author":"Gilbert","year":"2017","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/j.1525-142X.2005.05002.x","article-title":"Comprehensive survey of carapacial ridge-specific genes in turtle implies co-option of some regulatory genes in carapace evolution","volume":"7","author":"Kuraku","year":"2005","journal-title":"Evol. Dev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1111\/joa.12189","article-title":"Comparative study of the shell development of hard- and soft-shelled turtles","volume":"225","author":"Nagashima","year":"2014","journal-title":"J. Anat."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12565-011-0121-y","article-title":"Body plan of turtles: An anatomical, developmental and evolutionary perspective","volume":"87","author":"Nagashima","year":"2012","journal-title":"Anat. Sci. Int."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2107","DOI":"10.1038\/ncomms3107","article-title":"The endoskeletal origin of the turtle carapace","volume":"4","author":"Hirasawa","year":"2013","journal-title":"Nat. Commun."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/nature14900","article-title":"Evolutionary origin of the turtle skull","volume":"525","author":"Bever","year":"2015","journal-title":"Nature"},{"key":"ref_10","unstructured":"Carroll, C. (1988). Vertebrate Paleontology and Evolution, W H Freeman and Co."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1098\/rsbl.2010.0371","article-title":"Transitional fossils and the origin of turtles","volume":"6","author":"Lyson","year":"2010","journal-title":"Biol. Lett."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1038\/nature14472","article-title":"A Middle Triassic stem-turtle and the evolution of the turtle body plan","volume":"523","author":"Schoch","year":"2015","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nature07533","article-title":"An ancestral turtle from the Late Triassic of southwestern China","volume":"456","author":"Li","year":"2008","journal-title":"Nature"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1016\/j.cub.2013.05.003","article-title":"Evolutionary origin of the turtle shell","volume":"23","author":"Lyson","year":"2013","journal-title":"Curr. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1016\/j.mod.2017.04.555","article-title":"Acquisition of the turtle shell: Changes in developmental program behind the evolutionary novelty","volume":"145","author":"Kuratani","year":"2017","journal-title":"Mech. Dev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/s41586-018-0419-1","article-title":"A Triassic stem turtle with an edentulous beak","volume":"560","author":"Li","year":"2018","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1093\/icb\/31.4.616","article-title":"The Development and Evolution of the Turtle Body Plan, Inferring Intrinsic Aspects of the Evolutionary Process from Experimental Embryology","volume":"31","author":"Burke","year":"1991","journal-title":"Am. Zool."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/76469","article-title":"Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays","volume":"18","author":"Brenner","year":"2000","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/ng.2615","article-title":"The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan","volume":"45","author":"Wang","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1387\/ijdb.140296jp","article-title":"Comparative analysis of pleurodiran and cryptodiran turtle embryos depicts the molecular ground pattern of the turtle carapacial ridge","volume":"58","author":"Hirasawa","year":"2014","journal-title":"Int. J. Dev. Biol."},{"key":"ref_21","first-page":"558","article-title":"How the turtle forms its shell: A paracrine hypothesis of carapace formation","volume":"304","author":"Tan","year":"2005","journal-title":"J. Exp. Zool. Part B Mol. Dev. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"dev163824","DOI":"10.1242\/dev.163824","article-title":"Coordinated directional outgrowth and pattern formation by integration of Wnt5a and Fgf signaling in planar cell polarity","volume":"145","author":"Gao","year":"2018","journal-title":"Development"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"dev165902","DOI":"10.1242\/dev.165902","article-title":"Wnt signalling: Conquering complexity","volume":"145","author":"Wiese","year":"2018","journal-title":"Development"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1016\/j.gde.2013.05.003","article-title":"Planar cell polarity in vertebrate limb morphogenesis","volume":"23","author":"Gao","year":"2013","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0092-8674(00)81226-X","article-title":"Dishevelled activates JNK and discriminates between JNK pathways in planar polarity and wingless signaling","volume":"94","author":"Boutros","year":"1998","journal-title":"Cell"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1046\/j.1365-2443.2003.00662.x","article-title":"The receptor tyrosine kinase Ror2 is involved in non-canonical Wnt5a\/JNK signalling pathway","volume":"8","author":"Oishi","year":"2003","journal-title":"Genes Cells"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1093\/embo-reports\/kvf008","article-title":"JNK functions in the non-canonical Wnt pathway to regulate convergent extension movements in vertebrates","volume":"3","author":"Yamanaka","year":"2002","journal-title":"EMBO Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1016\/j.cub.2010.09.063","article-title":"WNT5A\/JNK and FGF\/MAPK pathways regulate the cellular events shaping the vertebrate limb bud","volume":"20","author":"Gros","year":"2010","journal-title":"Curr. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature10098","article-title":"Global quantification of mammalian gene expression control","volume":"473","author":"Busse","year":"2011","journal-title":"Nature"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nrm1488","article-title":"Molecular mechanisms of translational control","volume":"5","author":"Gebauer","year":"2004","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.cell.2009.01.042","article-title":"Regulation of translation initiation in eukaryotes: Mechanisms and biological targets","volume":"136","author":"Sonenberg","year":"2009","journal-title":"Cell"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"R168","DOI":"10.1016\/j.cub.2016.12.040","article-title":"The turtle\u2019s shell","volume":"27","author":"Cordero","year":"2017","journal-title":"Curr. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.pharmthera.2013.01.002","article-title":"The WNT signaling pathway from ligand secretion to gene transcription: Molecular mechanisms and pharmacological targets","volume":"138","author":"Baarsma","year":"2013","journal-title":"Pharmacol. Ther."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2625","DOI":"10.1128\/MCB.15.5.2625","article-title":"Identification of distinct classes and functional domains of Wnts through expression of wild-type and chimeric proteins in Xenopus embryos","volume":"15","author":"Du","year":"1995","journal-title":"Mol. Cell Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1016\/j.semcdb.2009.09.004","article-title":"Regulation of convergence and extension movements during vertebrate gastrulation by the Wnt\/PCP pathway","volume":"20","author":"Roszko","year":"2009","journal-title":"Semin. Cell. Dev. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/18899","article-title":"A new secreted protein that binds to Wnt proteins and inhibits their activities","volume":"398","author":"Hsieh","year":"1999","journal-title":"Nature"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1016\/j.jmb.2006.01.047","article-title":"NMR structure of the WIF domain of the human Wnt-inhibitory factor-1","volume":"357","author":"Liepinsh","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/34848","article-title":"Dickkopf-1 is a member of a new family of secreted proteins and functions in head induction","volume":"391","author":"Glinka","year":"1998","journal-title":"Nature"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"22429","DOI":"10.1074\/jbc.R600015200","article-title":"Wnt signaling: Multiple pathways, multiple receptors, and multiple transcription factors","volume":"281","author":"Gordon","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_41","first-page":"1516","article-title":"Wnt5a and Wnt11 regulate mammalian anterior-posterior axis elongation","volume":"142","author":"Andre","year":"2015","journal-title":"Development"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1016\/S0960-9822(03)00374-9","article-title":"Mutation of Celsr1 disrupts planar polarity of inner ear hair cells and causes severe neural tube defects in the mouse","volume":"13","author":"Curtin","year":"2003","journal-title":"Curr. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/nature09129","article-title":"Planar cell polarity breaks bilateral symmetry by controlling ciliary positioning","volume":"466","author":"Song","year":"2010","journal-title":"Nature"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1146\/annurev-cellbio-100814-125315","article-title":"Wnt-Frizzled\/planar cell polarity signaling: Cellular orientation by facing the wind (Wnt)","volume":"31","author":"Yang","year":"2015","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.devcel.2011.01.001","article-title":"Wnt signaling gradients establish planar cell polarity by inducing Vangl2 phosphorylation through Ror2","volume":"20","author":"Gao","year":"2011","journal-title":"Dev. Cell"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4044","DOI":"10.1073\/pnas.1200421109","article-title":"Wnt5a-Ror-Dishevelled signaling constitutes a core developmental pathway that controls tissue morphogenesis","volume":"109","author":"Ho","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1242\/dev.126.6.1211","article-title":"A Wnt5a pathway underlies outgrowth of multiple structures in the vertebrate embryo","volume":"126","author":"Yamaguchi","year":"1999","journal-title":"Development"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1016\/S0092-8674(05)80019-4","article-title":"Selective activation of the JNK signaling cascade and c-Jun transcriptional activity by the small GTPases Rac and Cdc42Hs","volume":"81","author":"Minden","year":"1995","journal-title":"Cell"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1126\/science.275.5298.400","article-title":"Reduced ubiquitin-dependent degradation of c-Jun after phosphorylation by MAP kinases","volume":"275","author":"Musti","year":"1997","journal-title":"Science"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1016\/S0092-8674(05)80018-2","article-title":"The small GTP-binding proteins Rac1 and Cdc42 regulate the activity of the JNK\/SAPK signaling pathway","volume":"81","author":"Coso","year":"1995","journal-title":"Cell"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1002\/jmor.1051990310","article-title":"Development of the turtle carapace: Implications for the evolution of a novel bauplan","volume":"199","author":"Burke","year":"1989","journal-title":"J. Morphol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1002\/jez.1401080304","article-title":"The proximo-distal sequence of origin of the parts of the chick wing and the role of the ectoderm","volume":"108","author":"SAUNDERS","year":"1948","journal-title":"J. Exp. Zool."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/nature00902","article-title":"Functions of FGF signalling from the apical ectodermal ridge in limb development","volume":"418","author":"Sun","year":"2002","journal-title":"Nature"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1146\/annurev.cellbio.20.010403.113126","article-title":"The Wnt signaling pathway in development and disease","volume":"20","author":"Logan","year":"2004","journal-title":"Annu. Rev. Cell. Dev. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1046\/j.1440-169x.1999.00466.x","article-title":"FGF10 can induce Fgf8 expression concomitantly with En1 and R-fng expression in chick limb ectoderm, independent of its dorsoventral specification","volume":"41","author":"Ohuchi","year":"1999","journal-title":"Dev. Growth Differ."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/0012-1606(73)90170-X","article-title":"A description of chick wing bud development and a model of limb morphogenesis","volume":"33","author":"Stark","year":"1973","journal-title":"Dev. Biol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.ydbio.2007.08.002","article-title":"A cellular lineage analysis of the chick limb bud","volume":"310","author":"Pearse","year":"2007","journal-title":"Dev. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3247","DOI":"10.1242\/dev.023176","article-title":"Wnt and FGF signals interact to coordinate growth with cell fate specification during limb development","volume":"135","author":"Brugmann","year":"2008","journal-title":"Development"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/0045-6039(84)90025-3","article-title":"Ectoderm as a determinant of early tissue pattern in the limb bud","volume":"15","author":"Solursh","year":"1984","journal-title":"Cell Differ."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"705","DOI":"10.2108\/zsj.18.705","article-title":"Normal Embryonic Stages of the Chinese Softshelled Turtle Pelodiscus sinensis (Trionychidae)","volume":"18","author":"Tokita","year":"2001","journal-title":"Zool. Sci."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"3033","DOI":"10.1242\/dev.109041","article-title":"The origin and loss of periodic patterning in the turtle shell","volume":"141","author":"Zimm","year":"2014","journal-title":"Development"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"8630","DOI":"10.1038\/s41598-018-26841-3","article-title":"Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)","volume":"8","author":"Zhang","year":"2018","journal-title":"Sci. Rep.-UK"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nature Biotechnol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"E10018","DOI":"10.1073\/pnas.1708433114","article-title":"Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation","volume":"114","author":"Bazin","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/s40168-021-01057-2","article-title":"Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost","volume":"9","author":"Liang","year":"2021","journal-title":"Microbiome"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13040-014-0034-0","article-title":"Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks","volume":"8","author":"Langdon","year":"2015","journal-title":"BioData Min."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nature21036","article-title":"Translation from unconventional 5\u2019 start sites drives tumour initiation","volume":"541","author":"Sendoel","year":"2017","journal-title":"Nature"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Li, B., and Dewey, C. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1093\/bib\/bbx153","article-title":"Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma","volume":"20","author":"Shahriyari","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"3179","DOI":"10.1021\/acs.jproteome.1c00051","article-title":"Prorocentrum donghaienseAutoactivation of Translation Causes the Bloom of in Harmful Algal Blooms","volume":"20","author":"Cao","year":"2021","journal-title":"J. Proteome Res."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1007\/s11427-020-1814-1","article-title":"Upregulation of the PPAR signaling pathway and accumulation of lipids are related to the morphological and structural transformation of the dragon-eye goldfish eye","volume":"64","author":"Yu","year":"2021","journal-title":"Sci. China Life Sci."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1495","DOI":"10.1016\/j.celrep.2014.05.002","article-title":"Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition","volume":"7","author":"Kronja","year":"2014","journal-title":"Cell Rep."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nprot.2007.514","article-title":"High-resolution in situ hybridization to whole-mount zebrafish embryos","volume":"3","author":"Thisse","year":"2008","journal-title":"Nat. Protoc."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"E203","DOI":"10.1073\/pnas.1317811111","article-title":"Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis","volume":"111","author":"Juntawong","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"110407","DOI":"10.1016\/j.cbpb.2020.110407","article-title":"Identification and functional analysis of SOX transcription factors in the genome of the Chinese soft-shell turtle (Pelodiscus sinensis)","volume":"242","author":"Zhang","year":"2020","journal-title":"Comp. Biochem. Phys. B"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Yuan, J., Reed, A., Chen, F., and Stewart, C. (2006). Statistical analysis of real-time PCR data. 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