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First insights into the giant panda ( A iluropoda melanoleuca ) blood transcriptome: a resource for novel gene loci and immunogenetics
Author(s) -
Du Lianming,
Li Wujiao,
Fan Zhenxin,
Shen Fujun,
Yang Mingyu,
Wang Zili,
Jian Zuoyi,
Hou Rong,
Yue Bisong,
Zhang Xiuyue
Publication year - 2015
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12367
Subject(s) - biology , kegg , ailuropoda melanoleuca , genetics , gene , sequence assembly , transcriptome , de novo transcriptome assembly , microsatellite , genome , gene expression , allele , ecology
The giant panda ( A iluropoda melanoleuca ) is one of the most famous flagship species for conservation, and its draft genome has recently been assembled. However, the transcriptome is not yet available. In this study, the blood transcriptomes of three pandas were characterized and about 160 million sequencing reads were generated using I llumina H i S eq 2000 paired‐end sequencing technology. The assembly yielded 92 598 transcripts with an average length of 1626 bp and N 50 length of 2842 bp. Based on a sequence similarity search against nonredundant (nr) protein database, a total of 38 522 (41.6%) transcripts were annotated. Of these annotated transcripts, 25 142 and 8272 transcripts were assigned to gene ontology terms and clusters of orthologous group, respectively. A search against the K yoto E ncyclopedia of G enes and G enomes P athway database ( KEGG ) indicated that 9098 (9.83%) transcripts mapped to 324 KEGG pathways, and the best represented functional categories of pathways were signal transduction and immune system. We have also identified 23 460 microsatellites, 43 560 SNP s as well as 21 456 alternative splicing events in the assembly. Additionally, a total of 24 341 complete open reading frames ( ORF s) were detected from the assembly where 1492 ORF s were found to be novel gene loci as these have not been annotated so far in any public database.