Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus

Singh, Tiratha Raj; Gupta, A.; Riju, Aikkal; Mahalaxmi, M.; Seal, Abhik; Arunachalam, V.

doi:10.1007/s12041-011-0052-3

Cited by 4 publications

(4 citation statements)

References 24 publications

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“…But in these cases, they are much lower than this generalized prediction as well as than those reported by Lepoittevin et al. (2010) and Singh et al. (2011) in eucalypts and other tree species.…”

Section: Discussioncontrasting

confidence: 64%

High‐throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform

Hendre¹,

Kamalakannan²,

Varghese³

2012

Plant Biotechnology Journal

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SummaryNext generation sequencing (NGS) technologies have revolutionized the pace and scale of genomics-and transcriptomics-based SNP discovery across different plant and animal species. Herein, 72-base paired-end Illumina sequencing was employed for high-throughput, parallel and large-scale SNP discovery in 41 growth-related candidate genes in Eucalyptus camaldulensis. Approximately 100 kb of genome from 96 individuals was amplified and sequenced using a hierarchical DNA ⁄ PCR pooling strategy and assembled over corresponding E. grandis reference. A total of 1191 SNPs (minimum 5% other allele frequency) were identified with an average frequency of 1 SNP ⁄ 83.9 bp, whereas in exons and introns, it was 1 SNP ⁄ 108.4 bp and 1 SNP ⁄ 65.6 bp, respectively. A total of 75 insertions and 89 deletions were detected of which approximately 15% were exonic. Transitions (Tr) were in excess than transversions (Tv) (Tr ⁄ Tv: 1.89), but exceeded in exons (Tr ⁄ Tv: 2.73). In exons, synonymous SNPs (Ka) prevailed over the non-synonymous SNPs (Ks; average Ka ⁄ Ks ratio: 0.72, range: 0-3.00 across genes). Many of the exonic SNPs ⁄ indels had potential to change amino acid sequence of respective genes. Transcription factors appeared more conserved, whereas enzyme coding genes appeared under relaxed control. Further, 541 SNPs were classified into 196 'equal frequency' (EF) blocks with almost similar minor allele frequencies to facilitate selection of one tag-SNP ⁄ EF-block. There were 241 (approximately 20%) 'zero-SNP' blocks with absence of SNPs in surrounding ±60 bp windows. The data thus indicated enormous extant and unexplored diversity in E. camaldulensis in the studied genes with potential applications for marker-trait associations.

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Section: Discussioncontrasting

confidence: 64%

High‐throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform

Hendre¹,

Kamalakannan²,

Varghese³

2012

Plant Biotechnology Journal

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“…In the present study, high number InDels in the size range of 1–24 nucleotides were documented in the three Eucalypts species at a frequency of 332.05, 359.08 and 420.54 bp per InDel in E. tereticornis, E. camaldulensis and E. grandis , respectively. This is higher than the earlier reported InDel frequency of 1.5 InDel/1000 bp [ 115 ] in Eucalyptus genome and 1/2756bp in inter-specific hybrid population [ 109 ]. Similarly, in Pinus taeda , Kong et al .…”

Section: Resultscontrasting

confidence: 66%

“…Insertion and deletion polymorphisms (InDels) are an important source of genomic variation in plant and animal genomes. Mechanisms such as insertion and excision of transposable elements, slippage in simple sequence replication, errors in DNA synthesis and repair, recombination and unequal crossover can result in the formation of InDels [ 114 – 115 ]. However, accurate genotyping from low-coverage sequence data can be challenging [ 116 ].…”

Section: Resultsmentioning

confidence: 99%

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

Dasgupta

Dharanishanthi

Agarwal³

et al. 2015

PLoS ONE

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The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.

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“…It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs) [9]. Other similar SNPs based plant specific databases provides good piece of information to the scientific community [10].…”

Section: Soybean Knowledge Base (Soykb)mentioning

confidence: 99%

Smdb: Soybean Marker Database

Kumar

Pratap

Udar

et al. 2014

International Journal for Computational Biology

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Soybean Marker Database (SMDB) is a repository of important genomic information for soybean. At present several genomic databases are available for plants. Some of the important oilseeds plant databases are ATPID database, Castor Bean Genome Database, CGPDB, SoyBase, Legume Information System (LIS), Brassica database, Sinbase, etc. To gain comprehensive information from varied amount of resources, we developed this database which provides general as well as specific information at universal level. Along with this it also furnishes gene level information for various functional categories such as transcription factor, disease resistant varieties, heat shock protein, genetically modified strain of soybean. The bunch of information available to researchers today increases in tremendous manner. Hence understanding the plant genome specific databases for acquiring specific information is the demand of time for crop improvement and research programmes. SMDB is designed for the purpose of exploring potential gene differences in different plant genotypes, including genetically modified and disease resistant crops beneficial to the farmer who cultivate this crop. SMDB

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Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus

Cited by 4 publications

References 24 publications

High‐throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform

High‐throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

Smdb: Soybean Marker Database

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