A genome database for a Japanese population of the larvacean Oikopleura dioica.
Y-chromosome
gene model
genome
larvacean
transcriptome
Journal
Development, growth & differentiation
ISSN: 1440-169X
Titre abrégé: Dev Growth Differ
Pays: Japan
ID NLM: 0356504
Informations de publication
Date de publication:
Aug 2020
Aug 2020
Historique:
received:
12
11
2019
revised:
10
06
2020
accepted:
10
06
2020
pubmed:
18
7
2020
medline:
1
1
2021
entrez:
18
7
2020
Statut:
ppublish
Résumé
The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
450-461Subventions
Organisme : JSPS KAKENHI
ID : 16H06279
Organisme : MEXT KAKENHI
ID : 221S0002
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 24870019
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 26840079
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 18K06256
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 26650079
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 15H04377
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 16K14735
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 17KT0023
Organisme : Grants-in-Aid for Scientific Research from the JSPS
ID : 19H03234
Organisme : Inamori Foundation (2015)
Organisme : Kato Memorial Research Foundation (2015-2016)
Organisme : Sumitomo Foundation (2016-2017)
Organisme : Japan Foundation for Applied Enzymology (2017, 2019)
Informations de copyright
© 2020 Japanese Society of Developmental Biologists.
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