ArticlePloS one2020
Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- GWAS for the identification of introgressed candidate genes ofFrontiers in plant science · 2024Article
- Microsatellite Markers: A Tool to Assess the Genetic Diversity of Yellow Mustard (Plants (Basel, Switzerland) · 2023Article
- The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis.International journal of molecular sciences · 2022Review
- Development of genome-specific SSR markers for the identification of introgressed segments of3 Biotech · 2022Article
- Development ofFrontiers in genetics · 2022Article
- Introgression and QTL mapping conferring resistance for Alternaria brassicae in the backcross progeny of Sinapis alba + Brassica juncea somatic hybrids.Plant cell reports · 2021Article
- Exploring the gene pool of Brassica napus by genomics-based approaches.Plant biotechnology journal · 2021Review
- Review on the Development and Applications of Medicinal Plant Genomes.Frontiers in plant science · 2021Review
- Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement inFrontiers in plant science · 2021Review
- Recent Findings Unravel Genes and Genetic Factors UnderlyingInternational journal of molecular sciences · 2020Review
- Development of a Yellow-Seeded Stable Allohexaploid Brassica Through Inter-Generic Somatic Hybridization With a High Degree of Fertility and Resistance toFrontiers in plant science · 2020Article
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Abstract
backgroundSinapis alba is a wild member of the Brassicaceae family reported to possess genetic resistance against major biotic and abiotic stresses of oilseed brassicas. However, the resistance nature of S. alba was not exploited generously due to the unavailability of usable genome sequences in public databases. Therefore, the present study was conducted to assemble the first draft genome from raw whole genome shotgun sequences with annotation and develop simple sequence repeat markers for molecular genetics and marker-assisted breeding.
resultsThe raw genome sequences had 96x coverage on the Illumina platform with 170 Gbp data. The developed assembly by SOAPdenovo2 has ~459 Mbp genome size covered in 403,423 contigs with an average size of 1138.04 bp. The assembly was BLASTX with Arabidopsis thaliana which showed 32.9% positive hits between both plants. The top hit species distribution analysis showed the highest similarity with A. thaliana. A total of 809,597 GO level annotations were recorded after BLASTX results, and 34,012 sequences were annotated with different enzyme codes grouped under seven classes. The gene prediction tool AUGUSTUS identified 113,107 probable genes with an average size of 684 bp. The biochemical pathway annotation assigned 16,119 potential genes to 152 KEGG maps and 1751 enzyme codes. The development of potential SSRs from the de-novo assembly yielded 70731 unique primer pairs. Out of 159 randomly selected SSR markers for validation, 149 successfully amplified in S. alba. However, 10 SSR markers did not amplify during the validation experiment.
conclusionThe annotated genome assembly with a large number of SSRs was developed in the present study. To the best of our knowledge, this is the first report of S. alba genome assembly development, annotation, and SSRs mining to date. The data presented here will be a very important resource for future crop improvement programs, especially for resistant breeding.
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