ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
Matija Brozovic
(1)
,
Christelle Dantec
(1)
,
Justine Dardaillon
(1)
,
Delphine Dauga
(2)
,
Emmanuel Faure
(3, 4)
,
Mathieu Gineste
(1)
,
Alexandra Louis
(5)
,
Magali Naville
(6)
,
Kazuhiro R. Nitta
(7)
,
Jacques Piette
(1)
,
Wendy Reeves
(8)
,
Celine Scornavacca
(9)
,
Paul Simion
(9)
,
Renaud Vincentelli
(10)
,
Maëlle Bellec
(11)
,
Sameh Ben Aicha
(12)
,
Marie Fagotto
(11)
,
Marion Gueroult-Bellone
(2)
,
Maximilian Haeussler
(13)
,
Edwin Jacox
(1)
,
Elijah K. Lowe
(14)
,
Mickaël Mendez
(7)
,
Alexis Roberge
(11)
,
Alberto Stolfi
(15)
,
Rui Yokomori
(16)
,
C. Titus Brown
(14)
,
Christian Cambillau
(10)
,
Lionel Christiaen
(17)
,
Frédéric Delsuc
(9)
,
Emmanuel J.P. Douzery
(9)
,
Rémi Dumollard
(12)
,
Takehiro Kusakabe
(18)
,
Kenta Nakai
(16)
,
Hiroki Nishida
(19)
,
Yutaka Satou
(20)
,
Billie Swalla
(14)
,
Michael Veeman
(8)
,
Jean-Nicolas Volff
(6)
,
Patrick Lemaire
(1, 3)
1
CRBM -
Centre de recherche en Biologie cellulaire de Montpellier
2 Bioself Communication [Marseille]
3 IBC - Institut de Biologie Computationnelle
4 IRIT-REVA - Real Expression Artificial Life
5 IBENS - Institut de biologie de l'ENS Paris
6 IGFL - Institut de Génomique Fonctionnelle de Lyon
7 IBDM - Institut de Biologie du Développement de Marseille
8 Kansas State University
9 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
10 AFMB - Architecture et fonction des macromolécules biologiques
11 UM - Université de Montpellier
12 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
13 Santa Cruz Genomics Institute
14 Michigan State University [East Lansing]
15 School of Biology [Atlanta]
16 UTokyo - The University of Tokyo
17 NYU - New York University [New York]
18 Konan University [Kobe, Japan]
19 Osaka University [Osaka]
20 Kyoto University
2 Bioself Communication [Marseille]
3 IBC - Institut de Biologie Computationnelle
4 IRIT-REVA - Real Expression Artificial Life
5 IBENS - Institut de biologie de l'ENS Paris
6 IGFL - Institut de Génomique Fonctionnelle de Lyon
7 IBDM - Institut de Biologie du Développement de Marseille
8 Kansas State University
9 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
10 AFMB - Architecture et fonction des macromolécules biologiques
11 UM - Université de Montpellier
12 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
13 Santa Cruz Genomics Institute
14 Michigan State University [East Lansing]
15 School of Biology [Atlanta]
16 UTokyo - The University of Tokyo
17 NYU - New York University [New York]
18 Konan University [Kobe, Japan]
19 Osaka University [Osaka]
20 Kyoto University
Delphine Dauga
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Emmanuel Faure
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Alexandra Louis
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Magali Naville
- Function : Author
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Celine Scornavacca
- Function : Author
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Paul Simion
- Function : Author
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Renaud Vincentelli
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Maëlle Bellec
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Christian Cambillau
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Lionel Christiaen
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Frédéric Delsuc
- Function : Author
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- IdRef : 078008395
Emmanuel J.P. Douzery
- Function : Author
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Rémi Dumollard
- Function : Author
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- IdHAL : remi-dumollard
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Hiroki Nishida
- Function : Author
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- ORCID : 0000-0002-7249-1668
Michael Veeman
- Function : Author
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- ORCID : 0000-0002-0752-6537
Patrick Lemaire
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Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
Domains
Modeling and Simulation
Origin : Publisher files allowed on an open archive
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