Guidelines for the nomenclature of genetic elements in tunicate genomes

Alberto Stolfi; Yasunori Sasakura; Domitille Chalopin; Yutaka Satou; Lionel Christiaen; Christelle Dantec; Toshinori Endo; Magali Naville; Hiroki Nishida; Billie J. Swalla; Jean Nicolas Volff; Ayelet Voskoboynik; Delphine Dauga; Patrick Lemaire

doi:10.1002/dvg.22822

Guidelines for the nomenclature of genetic elements in tunicate genomes

Alberto Stolfi, Yasunori Sasakura, Domitille Chalopin, Yutaka Satou, Lionel Christiaen, Christelle Dantec, Toshinori Endo, Magali Naville, Hiroki Nishida, Billie J. Swalla, Jean Nicolas Volff, Ayelet Voskoboynik, Delphine Dauga, Patrick Lemaire

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

Abstract

Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. genesis 53:65-78, 2015.

Original language	English (US)
Pages (from-to)	1-14
Number of pages	14
Journal	Genesis
Volume	53
Issue number	1
DOIs	https://doi.org/10.1002/dvg.22822
State	Published - Jan 1 2015

Keywords

Gene
Genome annotation
Transposable element
Tunicates
cis-regulatory sequences

ASJC Scopus subject areas

Genetics
Endocrinology
Cell Biology

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10.1002/dvg.22822

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abstract = "Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. genesis 53:65-78, 2015.",

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AU - Stolfi, Alberto

AU - Sasakura, Yasunori

AU - Chalopin, Domitille

AU - Satou, Yutaka

AU - Christiaen, Lionel

AU - Dantec, Christelle

AU - Endo, Toshinori

AU - Naville, Magali

AU - Nishida, Hiroki

AU - Swalla, Billie J.

AU - Volff, Jean Nicolas

AU - Voskoboynik, Ayelet

AU - Dauga, Delphine

AU - Lemaire, Patrick

PY - 2015/1/1

Y1 - 2015/1/1

N2 - Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. genesis 53:65-78, 2015.

AB - Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. genesis 53:65-78, 2015.

KW - Gene

KW - Genome annotation

KW - Transposable element

KW - Tunicates

KW - cis-regulatory sequences

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Guidelines for the nomenclature of genetic elements in tunicate genomes

Abstract

Keywords

ASJC Scopus subject areas

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