Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data

Yue, Jia-Xing; Li, Kun-Lung; Yu, Jr-Kai

doi:10.1016/j.margen.2015.03.010

Title: Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data

Journal Article · Tue Dec 01 00:00:00 EST 2015 · Marine Genomics

DOI:https://doi.org/10.1016/j.margen.2015.03.010· OSTI ID:1251661

Yue, Jia-Xing; Li, Kun-Lung; Yu, Jr-Kai

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1251661

Journal Information:: Marine Genomics, Journal Name: Marine Genomics Vol. 24 Journal Issue: P2; ISSN 1874-7787

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

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Cited by: 8 works

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References (48)

Primordial germ cells and oocytes of Branchiostoma virginiae (Cephalochordata, Acrania) are flagellated epithelial cells: relationship between epithelial and primary egg polarity Frick, Jennifer E.; Ruppert, Edward E. Zygote, Vol. 5, Issue 2 https://doi.org/10.1017/S0967199400003816	journal	May 1997
Early Development in the Lancelet (= Amphioxus) Branchiostoma floridae from Sperm Entry through Pronuclear Fusion: Presence of Vegetal Pole Plasm and Lack of Conspicuous Ooplasmic Segregation Holland, L. Z.; Holland, N. D. The Biological Bulletin, Vol. 182, Issue 1 https://doi.org/10.2307/1542182	journal	February 1992
Tunicates and not cephalochordates are the closest living relatives of vertebrates Delsuc, Frédéric; Brinkmann, Henner; Chourrout, Daniel Nature, Vol. 439, Issue 7079 https://doi.org/10.1038/nature04336	journal	February 2006
Small RNA regulation of reproductive function: SMALL RNA REGULATION Hale, Benjamin J.; Yang, Cai-Xia; Ross, Jason W. Molecular Reproduction and Development, Vol. 81, Issue 2 https://doi.org/10.1002/mrd.22272	journal	November 2013
A New Deep-water Lancelet (Cephalochordata) from off Cape Nomamisaki, SW Japan, with a Proposal of the Revised System Recovering the Genus Asymmetron Nishikawa, Teruaki Zoological Science, Vol. 21, Issue 11 https://doi.org/10.2108/zsj.21.1131	journal	November 2004
The stem cell system in demosponges: Insights into the origin of somatic stem cells: Stem cell system in demosponges Funayama, Noriko Development, Growth & Differentiation, Vol. 52, Issue 1 https://doi.org/10.1111/j.1440-169X.2009.01162.x	journal	January 2010
AnnotationSketch: a genome annotation drawing library Steinbiss, Sascha; Gremme, Gordon; Schärfer, Christin Bioinformatics, Vol. 25, Issue 4 https://doi.org/10.1093/bioinformatics/btn657	journal	December 2008
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
Ab initio Gene Finding in Drosophila Genomic DNA Salamov, Asaf A.; Solovyev, Victor V. Genome Research, Vol. 10, Issue 4, p. 516-522 https://doi.org/10.1101/gr.10.4.516	journal	April 2000
On the Interpretation of χ 2 from Contingency Tables, and the Calculation of P Fisher, R. A. Journal of the Royal Statistical Society, Vol. 85, Issue 1 https://doi.org/10.2307/2340521	journal	January 1922
Interstitial stem cells in Hydra: multipotency and decision-making David, Charles N. The International Journal of Developmental Biology, Vol. 56, Issue 6-7-8 https://doi.org/10.1387/ijdb.113476cd	journal	January 2012
At the Transition from Invertebrates to Vertebrates, a Novel GnRH-Like Peptide Emerges in Amphioxus Roch, Graeme J.; Tello, Javier A.; Sherwood, Nancy M. Molecular Biology and Evolution, Vol. 31, Issue 4 https://doi.org/10.1093/molbev/mst269	journal	December 2013
Versatile Germline Genes Juliano, C.; Wessel, G. Science, Vol. 329, Issue 5992 https://doi.org/10.1126/science.1194037	journal	August 2010
Patterns of molecular evolution of the germ line specification gene oskar suggest that a novel domain may contribute to functional divergence in Drosophila Ahuja, Abha; Extavour, Cassandra G. Development Genes and Evolution, Vol. 224, Issue 2 https://doi.org/10.1007/s00427-013-0463-7	journal	January 2014
Phylogenetic position of a whale-fall lancelet (Cephalochordata) inferred from whole mitochondrial genome sequences Kon, Takeshi; Nohara, Masahiro; Yamanoue, Yusuke BMC Evolutionary Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2148-7-127	journal	January 2007
A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus? Paps, J.; Holland, P. W. H.; Shimeld, S. M. Briefings in Functional Genomics, Vol. 11, Issue 2 https://doi.org/10.1093/bfgp/els012	journal	March 2012
The chordate amphioxus: an emerging model organism for developmental biology Holland, L. Z.; Laudet, V.; Schubert, M. Cellular and Molecular Life Sciences, Vol. 61, Issue 18 https://doi.org/10.1007/s00018-004-4075-2	journal	September 2004
Stem cell systems and regeneration in planaria Rink, Jochen C. Development Genes and Evolution, Vol. 223, Issue 1-2 https://doi.org/10.1007/s00427-012-0426-4	journal	November 2012
Evolution of the bilaterian germ line: lineage origin and modulation of specification mechanisms Extavour, C. G. M. Integrative and Comparative Biology, Vol. 47, Issue 5 https://doi.org/10.1093/icb/icm027	journal	June 2007
The amphioxus genome illuminates vertebrate origins and cephalochordate biology Holland, L. Z.; Albalat, R.; Azumi, K. Genome Research, Vol. 18, Issue 7 https://doi.org/10.1101/gr.073676.107	journal	July 2008
Laboratory Spawning and Development of the Bahama Lancelet, Asymmetron lucayanum (Cephalochordata): Fertilization Through Feeding Larvae Holland, Nicholas D.; Holland, Linda Z. The Biological Bulletin, Vol. 219, Issue 2 https://doi.org/10.1086/BBLv219n2p132	journal	October 2010
The fine structure of the growth stage oocytes of a lancelet (= amphioxus), Branchiostoma lanceolatum Holland, Nicholas D.; Holland, Linda Z. Invertebrate Reproduction & Development, Vol. 19, Issue 2 https://doi.org/10.1080/07924259.1991.9672164	journal	February 1991
The amphioxus genome and the evolution of the chordate karyotype Putnam, Nicholas H.; Butts, Thomas; Ferrier, David E. K. Nature, Vol. 453, Issue 7198 https://doi.org/10.1038/nature06967	journal	June 2008
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Conesa, A.; Gotz, S.; Garcia-Gomez, J. M. Bioinformatics, Vol. 21, Issue 18 https://doi.org/10.1093/bioinformatics/bti610	journal	August 2005
The Transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A Window into Chordate Evolution Yue, Jia-Xing; Yu, Jr-Kai; Putnam, Nicholas H. Genome Biology and Evolution, Vol. 6, Issue 10 https://doi.org/10.1093/gbe/evu212	journal	September 2014
Additional molecular support for the new chordate phylogeny Delsuc, Frédéric; Tsagkogeorga, Georgia; Lartillot, Nicolas genesis, Vol. 46, Issue 11 https://doi.org/10.1002/dvg.20450	journal	November 2008
Evolution of the germ line–soma relationship in vertebrate embryos Johnson, Andrew D.; Richardson, Emma; Bachvarova, Rosemary F. REPRODUCTION, Vol. 141, Issue 3 https://doi.org/10.1530/REP-10-0474	journal	March 2011
Asymmetric localization of germline markers Vasa and Nanos during early development in the amphioxus Branchiostoma floridae Wu, Hui-Ru; Chen, Yen-Ta; Su, Yi-Hsien Developmental Biology, Vol. 353, Issue 1 https://doi.org/10.1016/j.ydbio.2011.02.014	journal	May 2011
BMP and Delta/Notch signaling control the development of amphioxus epidermal sensory neurons: insights into the evolution of the peripheral sensory system Lu, Tsai-Ming; Luo, Yi-Jyun; Yu, Jr-Kai Development, Vol. 139, Issue 11 https://doi.org/10.1242/dev.073833	journal	June 2012
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Mechanisms of germ cell specification across the metazoans: epigenesis and preformation Extavour, Cassandra G.; Akam, Michael Development, Vol. 130, Issue 24 https://doi.org/10.1242/dev.00804	journal	December 2003
RNA Granules in Germ Cells Voronina, E.; Seydoux, G.; Sassone-Corsi, P. Cold Spring Harbor Perspectives in Biology, Vol. 3, Issue 12 https://doi.org/10.1101/cshperspect.a002774	journal	July 2011
EST and transcriptome analysis of cephalochordate amphioxus--past, present and future Wang, Y. -B.; Chen, S. -H.; Lin, C. -Y. Briefings in Functional Genomics, Vol. 11, Issue 2 https://doi.org/10.1093/bfgp/els002	journal	February 2012
oskar Predates the Evolution of Germ Plasm in Insects Ewen-Campen, Ben; Srouji, John R.; Schwager, Evelyn E. Current Biology, Vol. 22, Issue 23 https://doi.org/10.1016/j.cub.2012.10.019	journal	December 2012
Proteinortho: Detection of (Co-)orthologs in large-scale analysis Lechner, Marcus; Findeiß, Sven; Steiner, Lydia BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-124	journal	April 2011
How much does the amphioxus genome represent the ancestor of chordates? Louis, A.; Roest Crollius, H.; Robinson-Rechavi, M. Briefings in Functional Genomics, Vol. 11, Issue 2 https://doi.org/10.1093/bfgp/els003	journal	February 2012
Evolution of the Mitochondrial Genome in Cephalochordata as Inferred from Complete Nucleotide Sequences from Two Epigonichthys Species Nohara, Masahiro; Nishida, Mutsumi; Miya, Masaki Journal of Molecular Evolution, Vol. 60, Issue 4 https://doi.org/10.1007/s00239-004-0238-x	journal	April 2005
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix Price, M. N.; Dehal, P. S.; Arkin, A. P. Molecular Biology and Evolution, Vol. 26, Issue 7 https://doi.org/10.1093/molbev/msp077	journal	April 2009
Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae Takatori, Naohito; Butts, Thomas; Candiani, Simona Development Genes and Evolution, Vol. 218, Issue 11-12 https://doi.org/10.1007/s00427-008-0245-9	journal	September 2008
Evolutionary crossroads in developmental biology: amphioxus Bertrand, Stephanie; Escriva, Hector Development, Vol. 138, Issue 22 https://doi.org/10.1242/dev.066720	journal	November 2011
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes Huang, Shengfeng; Chen, Zelin; Yan, Xinyu Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6896	journal	December 2014
Expression of germline markers in three species of amphioxus supports a preformation mechanism of germ cell development in cephalochordates Zhang, Qiu-Jin; Luo, Yi-Jyun; Wu, Hui-Ru EvoDevo, Vol. 4, Issue 1 https://doi.org/10.1186/2041-9139-4-17	journal	January 2013
A conserved germline multipotency program Juliano, Celina E.; Swartz, S. Zachary; Wessel, Gary M. Development, Vol. 137, Issue 24 https://doi.org/10.1242/dev.047969	journal	December 2010
Closing the circle of germline and stem cells: the Primordial Stem Cell hypothesis Solana, Jordi EvoDevo, Vol. 4, Issue 1 https://doi.org/10.1186/2041-9139-4-2	journal	January 2013
Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida Bourlat, Sarah J.; Juliusdottir, Thorhildur; Lowe, Christopher J. Nature, Vol. 444, Issue 7115 https://doi.org/10.1038/nature05241	journal	October 2006
Bucky Ball Organizes Germ Plasm Assembly in Zebrafish Bontems, Franck; Stein, Amandine; Marlow, Florence Current Biology, Vol. 19, Issue 5 https://doi.org/10.1016/j.cub.2009.01.038	journal	March 2009
A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae Yu, Jr-Kai; Wang, Ming-Chih; Shin-I, Tadasu Development Genes and Evolution, Vol. 218, Issue 11-12 https://doi.org/10.1007/s00427-008-0228-x	journal	September 2008
The molecular machinery of germ line specification: GERM LINE MOLECULAR MACHINERY Ewen-Campen, Ben; Schwager, Evelyn E.; Extavour, Cassandra G. M. Molecular Reproduction and Development, Vol. 77, Issue 1 https://doi.org/10.1002/mrd.21091	journal	September 2009

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