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

Gui D, Jia K, Xia J, Yang L, Chen J, Wu Y, Yi M - PLoS ONE (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China ; School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. China.

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.

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Related in: MedlinePlus

GO assignment for assembled unigenes.The results are summarized in three main categories: biological process, cellular component and molecular function. In total, 37,976 unigenes were assigned to GO. Classified gene objects are depicted as absolute numbers of the total number of gene objects with GO assignments.
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pone-0072417-g003: GO assignment for assembled unigenes.The results are summarized in three main categories: biological process, cellular component and molecular function. In total, 37,976 unigenes were assigned to GO. Classified gene objects are depicted as absolute numbers of the total number of gene objects with GO assignments.

Mentions: GO (gene ontology) is an international classification system for standardized gene functions and is used to annotate and analyze gene functions and gene products in any organism. GO contains three main, independent ontologies: biological process, molecular function, and cellular component [17]. To predict their possible functions, the unigenes were searched against the GO database. We used the Blast2GO program [22] to analyze GO annotation of the assembled unigenes, and then applied the WEGO software to perform GO functional classifications [23]. Based on NR annotation, 37,976 unigenes were assigned to 61 GO terms belonging to three main GO ontologies (Fig. 3). Further analysis of the 61 GO terms showed that the dominant terms were “cellular processes”, “metabolic processes”, “cells”, “cell parts”, “organelles” and “binding”. Within the biological process group, the great majority was related to cellular process and metabolic process. Within cellular component, the largest proportion was assigned to cells and cell parts, followed by binding and catalytic activity. Remarkably, a few genes were related to immune system process and locomotion.


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

Gui D, Jia K, Xia J, Yang L, Chen J, Wu Y, Yi M - PLoS ONE (2013)

GO assignment for assembled unigenes.The results are summarized in three main categories: biological process, cellular component and molecular function. In total, 37,976 unigenes were assigned to GO. Classified gene objects are depicted as absolute numbers of the total number of gene objects with GO assignments.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3756080&req=5

pone-0072417-g003: GO assignment for assembled unigenes.The results are summarized in three main categories: biological process, cellular component and molecular function. In total, 37,976 unigenes were assigned to GO. Classified gene objects are depicted as absolute numbers of the total number of gene objects with GO assignments.
Mentions: GO (gene ontology) is an international classification system for standardized gene functions and is used to annotate and analyze gene functions and gene products in any organism. GO contains three main, independent ontologies: biological process, molecular function, and cellular component [17]. To predict their possible functions, the unigenes were searched against the GO database. We used the Blast2GO program [22] to analyze GO annotation of the assembled unigenes, and then applied the WEGO software to perform GO functional classifications [23]. Based on NR annotation, 37,976 unigenes were assigned to 61 GO terms belonging to three main GO ontologies (Fig. 3). Further analysis of the 61 GO terms showed that the dominant terms were “cellular processes”, “metabolic processes”, “cells”, “cell parts”, “organelles” and “binding”. Within the biological process group, the great majority was related to cellular process and metabolic process. Within cellular component, the largest proportion was assigned to cells and cell parts, followed by binding and catalytic activity. Remarkably, a few genes were related to immune system process and locomotion.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China ; School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. China.

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.

Show MeSH
Related in: MedlinePlus