De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery

PloS One
Tingxian DengXianwei Liang

Abstract

The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simp...Continue Reading

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Jan 23, 2020·Animal Genetics·Y ZhangJ S F Barker
Apr 14, 2019·Scientific Reports·Reena AroraRamesh Kumar Vijh
Aug 21, 2019·Frontiers in Genetics·Rachel YoungDavid A Hume
Jun 11, 2017·Scientific Reports·Zhigang LiRongjia Zhou

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Datasets Mentioned

BETA
GDJS00000000.1

Methods Mentioned

BETA
PCR

Software Mentioned

Trinity
EMBOSS
UPGMA
ORF Finder
FastQC
PowerMarker
Primer3
BLASTx
BLAST
Blast2GO

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