In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB

Sarika, .; Arora, Vasu; Iquebal, Mir Asif; Rai, Anil; Kumar, Dinesh

doi:10.1186/1471-2164-14-43

Cited by 19 publications

(10 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the present study, we identified a total of 99,293 microsatellites based on the whole-genome sequences of swamp eel. The distribution frequency of microsatellites (179/Mb) estimated in the genome is comparable to that documented in buffalo genome (170/Mb) 33 , but lower than those in human and mouse 34 . These differences could be due to the variation in search criteria, sizes of the databases and bioinformatics software tools used in different studies for identification of microsatellites.…”

Section: Discussionsupporting

confidence: 58%

See 1 more Smart Citation

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

Chen

Huang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.

show abstract

Section: Discussionsupporting

confidence: 58%

“…The genomic data are excellent sources for SSR mining and has been utilized in various species 9 , 25 , 32 , 33 . In the present study, we identified a total of 99,293 microsatellites based on the whole-genome sequences of swamp eel.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

Chen

Huang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…SSR markers have been demonstrated to be an extremely useful tool for investigating population clustering, genetic divergence, parentage testing, and genetic resource conservation[ 28 – 30 ]. Sarika et al [ 31 ] developed the first microsatellite database of the water buffalo, BuffSatDb ( http://cabindb.iasri.res.in/buffsatdb/ ), which is a web-based relational database of 910,529 microsatellite markers that was generated by in silico microsatellite mining and has helped in resolving the presence of degenerate bases in the current buffalo assembly. However, SSR markers that have been used in the analysis of genetic relationships and genetic variations of different buffaloes were mainly derived from other domesticated bovids [ 32 – 34 ], and no SSR markers of the swamp buffalo have been developed and reported to date.…”

Section: Introductionmentioning

confidence: 99%

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

Deng

Pang

et al. 2016

PLoS ONE

View full text Add to dashboard Cite

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.

show abstract

“…The rapid development of sequencing technologies allowed the obtention of complete genome sequences from an increasing number of species [30], which is an excellent source for identification of microsatellite markers already used in several species [30,31,32,33,34].…”

Section: Discussionmentioning

confidence: 99%

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

Gomes

Aguiar

Cabral

et al. 2020

Preprint

View full text Add to dashboard Cite

A broad panel of potentially amplifiable microsatellite loci and a multiplex system were developed for the Amazonian symbol fish species Arapaima gigas, which is currently in high danger of extinction due to the disorderly fishing exploitation. Several factors have contributed to the increase of this threat, among which we highlight the lack of genetic information about the structure and taxonomic status of the species, as well as the lack of accurate tools for evaluation of the effectivity of current management programs. Based on Arapaima gigas’ whole genome, available at the NCBI database (ID: 12404), a total of 95,098 unique perfect microsatellites were identified, including their proposed primers. From this panel, a multiplex system containing 12 tetranucleotide microsatellite markers was validated. These tools are valuable for research in as many areas as bioinformatics, ecology, genetics, evolution and comparative studies, since they are able to provide more accurate information for fishing management, conservation of wild populations and genetic management of aquaculture.

show abstract

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB

Cited by 19 publications

References 24 publications

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

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

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

Contact Info

Product

Resources

About