Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus

Scientific Data
Yong Yan LiaoJun Feng Han

Abstract

Chinese horseshoe crabs (Tachypleus tridentatus), ancient marine arthropods dating back to the mid-Palaeozoic Era, have provided valuable resources for the detection of bacterial or fungal contamination. However, excessive exploitation for the amoebocyte lysate of Tachypleus has dramatically decreased the population of the Chinese horseshoe crabs. Thus, we present sequencing, assembly and annotation of T. tridentatus, with the hope of understanding the genomic feature of the living fossil and assisting scientists with the protection of this endangered species. The final genome contained a total size of 1.943 Gb, covering 90.23% of the estimated genome size. The transcriptome of three larval stages was constructed to investigate the candidate gene involved in the larval development and validate annotation. The completeness of the genome and gene models was estimated by BUSCO, reaching 96.2% and 95.4%, respectively. The synonymous substitution distribution of paralogues revealed that T. tridentatus had undergone two rounds of whole-genome duplication. All genomic and transcriptome data have been deposited in public databases, ready to be used by researchers working on horseshoe crabs.

References

Jul 21, 1975·Chromosoma·R B GoldbergE H Davidson
Jan 1, 1996·Molecular Biology and Evolution·S V Muse
Dec 10, 1998·Nucleic Acids Research·F CorpetD Kahn
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Dec 11, 1999·Nucleic Acids Research·T K AttwoodW Wright
Dec 11, 1999·Nucleic Acids Research·J SchultzP Bork
Feb 13, 2001·Trends in Cell Biology·P BurkhardS V Strelkov
Apr 5, 2002·Genome Research·W James Kent
May 29, 2002·Nature Genetics·Aoife McLysaghtKenneth H Wolfe
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
May 18, 2004·BMC Bioinformatics·Ian Korf
Dec 21, 2004·Nucleic Acids Research·Huaiyu MiPaul D Thomas
Mar 9, 2005·Current Opinion in Plant Biology·Keith L Adams, Jonathan F Wendel
Apr 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Steven MaereYves Van de Peer
Jul 5, 2005·Lab Animal·Stephen A Smith, Jim Berkson
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 29, 2007·Genomics, Proteomics & Bioinformatics·Zhang ZhangJun Yu
Nov 16, 2007·Nucleic Acids Research·Nicolas HuloChristian J A Sigrist
Jan 26, 2008·Bioinformatics·Mario StankeDavid Haussler
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Nov 20, 2012·Nucleic Acids Research·Christian J A SigristIoannis Xenarios
Dec 1, 2012·Nucleic Acids Research·Daniel H HaftErin Beck
Apr 20, 2013·Nature·Chris T AmemiyaKerstin Lindblad-Toh
Oct 17, 2013·Nature Communications·Zhijian CaoWenxin Li
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
May 8, 2014·Nature Communications·Kristian W SanggaardJun Wang
Dec 17, 2014·Current Protocols in Bioinformatics·Michael S CampbellMark Yandell
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Jun 6, 2015·Mobile DNA·Weidong BaoOleksiy Kohany
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Feb 10, 2016·Nature Communications·Monika Gulia-NussCatherine A Hill
Jun 25, 2016·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Kevin N ChesmoreChristopher C Chabot
Aug 26, 2016·Nature Protocols·Mihaela PerteaSteven L Salzberg

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Citations

Jul 30, 2020·Molecular Ecology Resources·Prashant ShingateByrappa Venkatesh
Jan 14, 2020·Development Genes and Evolution·Erik D NolanPrashant P Sharma
May 10, 2020·Nature Communications·Prashant ShingateByrappa Venkatesh
Jun 10, 2021·Mitochondrial DNA. Part B, Resources·Maria E SarmientoNik Soriani Yaacob

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Methods Mentioned

BETA
PCR
RNA-Seq

Software Mentioned

HISAT2
BUSCO
CODEML
Python
InterProScan
KaKs Calculator
MAKER
GapCloser
SAMtools
ProSitePatterns

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