The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.
Zhanjiang Liu,Shikai Liu,Jun Yao,Lisui Bao,Jiaren Zhang,Yun Li,Chen Jiang,Luyang Sun,Ruijia Wang,Yu Zhang,Tao Zhou,Qifan Zeng,Qiang Fu,Sen Gao,Ning Li,Sergey Koren,Yanliang Jiang,Aleksey V. Zimin,Peng Xu,Adam M. Phillippy,Xin Geng,Lin Song,Fanyue Sun,Chao Li,Xiaozhu Wang,Ailu Chen,Yulin Jin,Zihao Yuan,Yujia Yang,Suxu Tan,Eric Peatman,Jianguo Lu,Zhenkui Qin,Rex A. Dunham,Zhaoxia Li,Tad S. Sonstegard,Jianbin Feng,Roy G. Danzmann,Steven Schroeder,Brian E. Scheffler,Mary V. Duke,Linda L. Ballard,Huseyin Kucuktas,Ludmilla Kaltenboeck,Haixia Liu,Jonathan W. Armbruster,Yangjie Xie,Mona L. Kirby,Yi Tian,Mary Elizabeth Flanagan,Weijie Mu,Geoffrey C. Waldbieser +51 more
TLDR
A high-quality reference genome sequence of channel catfish is reported, providing evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish and demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.Abstract:
Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance. Catfish represent 6.3% of all vertebrate species, and occupy a phylogenetic position close to the common ancestor of bony fish. Liu et al. present a reference genome of the channel catfish, and reveal a genomic basis for the evolutionary loss of scales in these species.read more
Citations
More filters
Journal ArticleDOI
Penaeid shrimp genome provides insights into benthic adaptation and frequent molting
Xiaojun Zhang,Jianbo Yuan,Yamin Sun,Shihao Li,Yi Gao,Yang Yu,Chengzhang Liu,Quanchao Wang,Xinjia Lv,Xiaoxi Zhang,Ka Yan Ma,Xiaobo Wang,Wenchao Lin,Long Wang,Xueli Zhu,Chengsong Zhang,Jiquan Zhang,Songjun Jin,Kuijie Yu,Jie Kong,Peng Xu,Jack Chen,Hong-Bin Zhang,Patrick Sorgeloos,Amir Sagi,Acacia Alcivar-Warren,Zhanjiang Liu,Lei Wang,Jue Ruan,Ka Hou Chu,Bin Liu,Fuhua Li,Jianhai Xiang +32 more
TL;DR: The authors provide a reference genome assembly, and show that gene expansion is involved in the regulation of frequent molting as well as benthic adaptation of the shrimp.
Journal ArticleDOI
Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB
TL;DR: The ultimate goals of database development are to provide infrastructure for data collection, curation, and annotation, and more importantly, to support innovated data structure for new types of data mining, data reanalysis, and networked genetic analysis that lead to the generation of new knowledge.
Journal ArticleDOI
Nutrigenomics and immune function in fish: new insights from omics technologies.
Samuel A.M. Martin,Elżbieta Król +1 more
TL;DR: Although great progress has been made to define the changes in host immune function, understanding the interplay between fish nutrition, intestinal microbiome and immune system is only just beginning to emerge.
Journal ArticleDOI
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research
Hisham A. Abdelrahman,Mohamed ElHady,Acacia Alcivar-Warren,Standish K. Allen,Rafet Al-Tobasei,Lisui Bao,Ben Beck,Harvey D. Blackburn,Brian G. Bosworth,John Buchanan,Jesse A. Chappell,William H. Daniels,Sheng Dong,Rex A. Dunham,Evan Durland,Ahmed Elaswad,Marta Gomez-Chiarri,Kamal Gosh,Ximing Guo,Perry B. Hackett,Terry Hanson,Dennis Hedgecock,Tiffany S. Howard,Leigh Holland,Molly Jackson,Yulin Jin,Karim Khalil,Thomas D. Kocher,Timothy D. Leeds,Ning Li,Lauren Lindsey,Shikai Liu,Zhanjiang Liu,Kyle E. Martin,Romi Novriadi,Ramjie Odin,Yniv Palti,Eric Peatman,Dina A. Proestou,Guyu Qin,Benjamin J. Reading,Caird E. Rexroad,Steven B. Roberts,Mohamed Salem,Andrew J. Severin,Huitong Shi,Craig A. Shoemaker,Sheila Stiles,Suxu Tan,Kathy F.J. Tang,Wilawan Thongda,Terrence R. Tiersch,Joseph R. Tomasso,Wendy Tri Prabowo,Roger L. Vallejo,Hein van der Steen,Khoi Vo,Geoff Waldbieser,Han-Ping Wang,Xiaozhu Wang,Jianhai Xiang,Yujia Yang,Roger Yant,Zihao Yuan,Qifan Zeng,Tao Zhou +65 more
TL;DR: A general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding is provided, with a focus on major Aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp.
Journal ArticleDOI
Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics.
TL;DR: It is highlighted that chromosome‐scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns, to generate predictable broad‐scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome.
References
More filters
Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Journal ArticleDOI
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Journal ArticleDOI
Circos: An information aesthetic for comparative genomics
Martin Krzywinski,Jacqueline E. Schein,Inanc Birol,Joseph M. Connors,Randy D. Gascoyne,Doug Horsman,Steven J.M. Jones,Marco A. Marra +7 more
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Journal ArticleDOI
Mammal Species of the World: A Taxonomic and Geographic Reference
TL;DR: Wilson and Reeder's Mammal Species of the World as discussed by the authors is the classic reference book on the taxonomic classification and distribution of more than 5400 species of mammals that exist today.
Related Papers (5)
The Atlantic salmon genome provides insights into rediploidization
Sigbjørn Lien,Ben F. Koop,Simen Rød Sandve,Jason R. Miller,Matthew Peter Kent,Torfinn Nome,Torgeir R. Hvidsten,Torgeir R. Hvidsten,Jong S. Leong,David R. Minkley,Aleksey V. Zimin,Fabian Grammes,Harald Grove,Arne B. Gjuvsland,Brian P. Walenz,Russell A. Hermansen,Russell A. Hermansen,Kristian R. von Schalburg,Eric Rondeau,Alex Di Genova,Jeevan Karloss Antony Samy,Jon Olav Vik,Magnus Dehli Vigeland,Lis Caler,Unni Grimholt,Sissel Jentoft,Dag Inge Våge,Pieter J. de Jong,Thomas Moen,Matthew Baranski,Yniv Palti,Douglas W. Smith,James A. Yorke,Alexander J. Nederbragt,Ave Tooming-Klunderud,Kjetill S. Jakobsen,Xuanting Jiang,Dingding Fan,Yan Hu,David A. Liberles,Richard Vidal,Patricia Iturra,Steven J.M. Jones,Steven J.M. Jones,Inge Jonassen,Alejandro Maass,Stig W. Omholt,William S. Davidson +47 more
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates
Camille Berthelot,Frédéric Brunet,Domitille Chalopin,Amélie Juanchich,Maria Bernard,Benjamin Noel,Pascal Bento,Corinne Da Silva,Karine Labadie,Adriana Alberti,Jean-Marc Aury,Alexandra Louis,Patrice Dehais,Philippe Bardou,Jérôme Montfort,Christophe Klopp,Cédric Cabau,Christine Gaspin,Gary H. Thorgaard,Mekki Boussaha,Edwige Quillet,René Guyomard,Delphine Galiana,Julien Bobe,Jean-Nicolas Volff,Carine Genet,Patrick Wincker,Olivier Jaillon,Hugues Roest Crollius,Yann Guiguen +29 more
Trimmomatic: a flexible trimmer for Illumina sequence data
The zebrafish reference genome sequence and its relationship to the human genome.
Kerstin Howe,Matthew D. Clark,Carlos Torroja,Carlos Torroja,James Torrance,Camille Berthelot,Matthieu Muffato,John E. Collins,Sean Humphray,Karen McLaren,Lucy Matthews,Stuart McLaren,Ian M Sealy,Mario Caccamo,Carol Churcher,Carol Scott,Jeffrey C. Barrett,Romke Koch,Gerd Jörg Rauch,Simon D. M. White,William Chow,Britt Kilian,Leonor T. Quintais,José Afonso Guerra-Assunção,Yi Zhou,Yong Gu,Jennifer Yen,Jan Hinnerk Vogel,Tina Eyre,Seth Redmond,Ruby Banerjee,Jianxiang Chi,Beiyuan Fu,Elizabeth Langley,Sean Maguire,Gavin K. Laird,D. M. Lloyd,Emma J. Kenyon,Sarah Donaldson,Harminder Sehra,Jeff Almeida-King,Jane E. Loveland,Stephen J. Trevanion,Matthew Jones,Michael A. Quail,Dave Willey,Adrienne Hunt,John Burton,Sarah Sims,Kirsten McLay,Bob Plumb,J. C. Davis,Chris Clee,Karen Oliver,Richard M. Clark,Clare Riddle,David Eliott,Glen Threadgold,Glenn Harden,Darren Ware,Beverly Mortimer,Giselle Kerry,Paul Heath,Benjamin Phillimore,Alan Tracey,N Corby,Matthew Dunn,Christopher M. Johnson,Jonathan Wood,Susan J. Clark,Sarah Pelan,Guy Griffiths,Michelle Smith,Rebecca Glithero,Philip Howden,Nick Barker,Christopher Stevens,Joanna Harley,Karen Holt,Georgios Panagiotidis,J Lovell,Helen Beasley,Carl Henderson,Daria Gordon,Katherine Auger,Debbie E. Wright,Joanna Collins,Claire Raisen,Lauren Dyer,Kenric Leung,Lauren Robertson,Kirsty Ambridge,Daniel Leongamornlert,Sarah McGuire,Ruth Gilderthorp,C Griffiths,Deepa Manthravadi,Sarah Nichol,Gary L A Barker,S. Whitehead,Michael Kay,Jacqueline Brown,Clare Murnane,Emma Gray,Matthew Humphries,N Sycamore,Darren Barker,David S. Saunders,J. M. Wallis,A K Babbage,S Hammond,M Mashreghi-Mohammadi,Lucy Barr,Sancha Martin,Paul Wray,Andrew D. Ellington,Nicholas Matthews,Matthew Ellwood,Rebecca Woodmansey,Graham Clark,James D. Cooper,A Tromans,Darren Grafham,C. D. Skuce,Richard Pandian,Robert Andrews,Elliot Harrison,A M Kimberley,J Garnett,Nigel Fosker,Rebekah Hall,P Garner,Daniel P. Kelly,Christine P. Bird,Sophie Palmer,Ines Gehring,Andrea Berger,Christopher M. Dooley,Christopher M. Dooley,Zübeyde Ersan-Ürün,Cigdem Eser,Horst Geiger,Maria Geisler,Lena Karotki,Anette Kirn,Judith Konantz,Martina Konantz,Martina Oberländer,Silke Rudolph-Geiger,Mathias Teucke,Kazutoyo Osoegawa,Baoli Zhu,Amanda Rapp,Sara Widaa,Cordelia Langford,Fengtang Yang,Nigel P. Carter,Jennifer Harrow,Zemin Ning,Javier Herrero,Steve Searle,Anton J. Enright,Robert Geisler,Robert Geisler,Ronald H.A. Plasterk,Charles Lee,Monte Westerfield,Pieter J. de Jong,Leonard I. Zon,John H. Postlethwait,Christiane Nüsslein-Volhard,Tim Hubbard,Hugues Roest Crollius,Jane Rogers,Derek L. Stemple +174 more