Journal
MOLECULAR ECOLOGY RESOURCES
Volume 15, Issue 4, Pages 1001-1013Publisher
WILEY
DOI: 10.1111/1755-0998.12367
Keywords
alternative splicing; giant panda; immune system; RNA-seq; transcriptome
Funding
- Chengdu Panda Breeding Research Foundation (CPF)
- National Science and Technology Support Project of China [2012BAC01B06]
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The giant panda (Ailuropoda 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 Illumina HiSeq 2000 paired-end sequencing technology. The assembly yielded 92598 transcripts with an average length of 1626bp and N50 length of 2842bp. Based on a sequence similarity search against nonredundant (nr) protein database, a total of 38522 (41.6%) transcripts were annotated. Of these annotated transcripts, 25142 and 8272 transcripts were assigned to gene ontology terms and clusters of orthologous group, respectively. A search against the Kyoto Encyclopedia of Genes and Genomes Pathway 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 23460 microsatellites, 43560 SNPs as well as 21456 alternative splicing events in the assembly. Additionally, a total of 24341 complete open reading frames (ORFs) were detected from the assembly where 1492 ORFs were found to be novel gene loci as these have not been annotated so far in any public database.
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