title: First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics.
abstract: 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 92 598 transcripts with an average length of 1626 bp and N50 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 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 23 460 microsatellites, 43 560 SNPs as well as 21 456 alternative splicing events in the assembly. Additionally, a total of 24 341 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.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Lianming
authors.initials: L
authors.lastname: Du
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Wujiao
authors.initials: W
authors.lastname: Li
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Zhenxin
authors.initials: Z
authors.lastname: Fan
authors.affiliation: The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China.
authors.forename: Fujun
authors.initials: F
authors.lastname: Shen
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Yang
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Zili
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Zuoyi
authors.initials: Z
authors.lastname: Jian
authors.affiliation: The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, 610081, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Hou
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Bisong
authors.initials: B
authors.lastname: Yue
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, China.
authors.forename: Xiuyue
authors.initials: X
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001773:Blood Cells / Q000276:immunology* / Q000502:physiology*; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D007125:Immunogenetics; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D015398:Signal Transduction / Q000235:genetics; D001503:Ursidae
keywords: RNA-seq; alternative splicing; giant panda; immune system; transcriptome