ArticlePloS one2016
De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.Molecular ecology · 2025Article
- Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover (Life (Basel, Switzerland) · 2022Article
- Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina).G3 (Bethesda, Md.) · 2022Article
- Novel Insight into the Potential Role of Acylglycerophosphate Acyltransferases Family Members on Triacylglycerols Synthesis in Buffalo.International journal of molecular sciences · 2022Article
- pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites.Life science alliance · 2022Article
- Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo.Genes · 2022Article
- Article
- Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer.PloS one · 2022Article
- Article
- Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis.Scientific reports · 2019Article
- Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation.Scientific reports · 2019Article
- A Gene Expression Atlas of the Domestic Water Buffalo (Frontiers in genetics · 2019Article
- Article
- De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese EndemicGenes · 2018Article
- De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery.Genes & genomics · 2018Article
- Illumina-based de novo transcriptome sequencing and analysis of Chinese forest musk deer.Journal of genetics · 2017Article
- Article
- Genome-wide mapping and characterization of microsatellites in the swamp eel genome.Scientific reports · 2017Article
- Article
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Authors and funding
10 authors.
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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 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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