Dataset Information

De novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response.

ABSTRACT:

Background

The Indo-Pacific humpback dolphin (Sousa chinensis), a marine mammal species inhabited in the waters of Southeast Asia, South Africa and Australia, has attracted much attention because of the dramatic decline in population size in the past decades, which raises the concern of extinction. So far, this species is poorly characterized at molecular level due to little sequence information available in public databases. Recent advances in large-scale RNA sequencing provide an efficient approach to generate abundant sequences for functional genomic analyses in the species with un-sequenced genomes.

Principal findings

We performed a de novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome by Illumina sequencing. 108,751 high quality sequences from 47,840,388 paired-end reads were generated, and 48,868 and 46,587 unigenes were functionally annotated by BLAST search against the NCBI non-redundant and Swiss-Prot protein databases (E-value<10(-5)), respectively. In total, 16,467 unigenes were clustered into 25 functional categories by searching against the COG database, and BLAST2GO search assigned 37,976 unigenes to 61 GO terms. In addition, 36,345 unigenes were grouped into 258 KEGG pathways. We also identified 9,906 simple sequence repeats and 3,681 putative single nucleotide polymorphisms as potential molecular markers in our assembled sequences. A large number of unigenes were predicted to be involved in immune response, and many genes were predicted to be relevant to adaptive evolution and cetacean-specific traits.

Conclusion

This study represented the first transcriptome analysis of the Indo-Pacific humpback dolphin, an endangered species. The de novo transcriptome analysis of the unique transcripts will provide valuable sequence information for discovery of new genes, characterization of gene expression, investigation of various pathways and adaptive evolution, as well as identification of genetic markers.

SUBMITTER: Gui D

PROVIDER: S-EPMC3756080 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

De novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response.

Gui Duan D Jia Kuntong K Xia Jia J Yang Lili L Chen Jialin J Wu Yuping Y Yi Meisheng M

PloS one 20130828 8

<h4>Background</h4>The Indo-Pacific humpback dolphin (Sousa chinensis), a marine mammal species inhabited in the waters of Southeast Asia, South Africa and Australia, has attracted much attention because of the dramatic decline in population size in the past decades, which raises the concern of extinction. So far, this species is poorly characterized at molecular level due to little sequence information available in public databases. Recent advances in large-scale RNA sequencing provide an effic ...[more]

PMID: 24015242

Similar Datasets

Project description:BACKGROUND:Subspecies recognition can affect how people (scientists and non-scientists alike) view organisms and thus has important implications for research on, as well as the conservation of, these entities. Recently, a small group of Indo-Pacific humpback dolphins was discovered inhabiting the waters off central western Taiwan. This geographically isolated population possesses pigmentation patterns that are subtly, but noticeably, different from their nearest conspecifics in the neighbouring waters of the Jiulong River Estuary and Pearl River Estuary of mainland China. Due to this population's low and declining numbers and the numerous threats it faces, it was assessed as critically endangered by the Red List of Threatened Species of the International Union for Conservation of Nature. The purpose of this study is to examine the degree of differentiation of the Taiwanese population to determine if subspecies recognition iswarranted. RESULTS:Analysis of the degree of differentiation in pigmentation patterns revealed nearly non-overlapping distributions between dolphins from Taiwanese waters and those from the Jiulong River + Pearl River estuaries of mainland China (the nearest known populations). The Taiwanese dolphins were clearly diagnosable from those of the Jiulong River + Pearl Riverestuaries under the most commonly accepted '75%rule' for subspecies delimitation (with 94% of one group being separable from 99+% of the other). Evidence of geographical isolation and behavioural differences also provided additional support for the distinctiveness of the Taiwanese dolphins. CONCLUSIONS:Together, the evidence strongly demonstrated that the Taiwanese humpback dolphin population is differentiated at the subspecies level and on an evolutionary trajectory that is independent from that of dolphins from adjacent waters of mainland China (i.e. Jiulong River + Pearl River estuaries). As a result, the taxonomy of Sousa chinensis was revised to include two subspecies: the Taiwanese humpback dolphin, Sousa chinensis taiwanensis subsp. nov., and the Chinese humpback dolphin, Sousa chinensis chinensis (the nominotypical subspecies). These subspecies are described, and the holotype and paratype specimens for S. c. taiwanensis are established.

Dataset Information

De novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response.

Background

Principal findings

Conclusion

Publications

De novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets