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<p>Genetic variation that results in phenotypic change is the most valuable asset of biological research, extending from the genome to eco-physiological context. Decoding the genetic basis of morphogenesis and phenotype development (genetic architecture) of elite germplasm is crucial for understanding the complex system of gene-ecosystem interactions. Re-construction of repository RNA-Seq datasets is considered to be an exclusive approach for decoding genetic architecture. Currently, a huge number of transcriptome datasets across the organisms are available; however, data analysis and interpretation remain challenging due to a lack of essential coding skills, computational resources, and expensive automated software. Seri-genetic resource comprises a wide range of phenotypes of <i>Morus</i> L. (mulberry) and <i>Bombyx mori</i> L. (silkworm); therefore objectives of the present study are (1) to optimize a stable, reproducible and user-friendly workflow for RNA-Seq analysis; and (2) to elucidate the genetic basis of phenotype of elite genetic resources. Here we have taken advantage of repository RNA-Seq datasets of integument tissue of <i>black dilute</i> (<i>bd</i>) homozygotes (<i>bd</i>/<i>bd</i>), heterozygotes mutant (+/<i>bd</i>), wild-type Dazao of <i>Bombyx</i><i> mori</i> L. (silkworm), and mature leaf tissue of three cytotypes <i>Morus</i> spp. (mulberry) including <i>M. notabilis</i> ( diploid), <i>M. indica</i> L. (diploid), <i>M. serrata</i> Roxb. (polyploid). Developed workflow emphasized an in-depth description of each state-of-the-art system/tool, downstream analysis including the authenticity of the taxonomic identity of the transcriptome, global transcriptome map/ network, and functional enrichment of overrepresented genes. The present data-mining approach indicates that <i>bd</i> silkworm mutants are associated with tyrosine (Try) degradation and melanogenesis, which might be mediated by the <i>dopachrome tautomerase</i> (<i>DTC</i>). On the other hand, <i>M. serrata</i> showed overrepresented genes significantly enriched in polyploid-associated functions, including nucleic acid metabolism, intrinsic activity of transposable elements, and functions connected to chloroplasts. Considering all, the present user-friendly workflow helps to identify the molecular evidence for a possible link between the phenome and transcriptome without prior coding knowledge and cost.</p>

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Decoding the Genetic Basis of Phenotype of Mutant Seri-Genetic Germplasm Resources Using Repository RNA-Seq Datasets: A Data Mining Workflow

  • 期刊论文

  • 发表日期：

    2026年3月30日

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  • Raju Mondal,
  • Ritwika Sur Chaudhuri,
  • Tanya Ahmed Sheik,
  • Lokesh Gangadharaiah,
  • Deepak Vijayan,
  • Nishitha Naik V.,
  • Manthira Moorthy S.

摘要

Genetic variation that results in phenotypic change is the most valuable asset of biological research, extending from the genome to eco-physiological context. Decoding the genetic basis of morphogenesis and phenotype development (genetic architecture) of elite germplasm is crucial for understanding the complex system of gene-ecosystem interactions. Re-construction of repository RNA-Seq datasets is considered to be an exclusive approach for decoding genetic architecture. Currently, a huge number of transcriptome datasets across the organisms are available; however, data analysis and interpretation remain challenging due to a lack of essential coding skills, computational resources, and expensive automated software. Seri-genetic resource comprises a wide range of phenotypes of Morus L. (mulberry) and Bombyx mori L. (silkworm); therefore objectives of the present study are (1) to optimize a stable, reproducible and user-friendly workflow for RNA-Seq analysis; and (2) to elucidate the genetic basis of phenotype of elite genetic resources. Here we have taken advantage of repository RNA-Seq datasets of integument tissue of black dilute (bd) homozygotes (bd/bd), heterozygotes mutant (+/bd), wild-type Dazao of Bombyx mori L. (silkworm), and mature leaf tissue of three cytotypes Morus spp. (mulberry) including M. notabilis ( diploid), M. indica L. (diploid), M. serrata Roxb. (polyploid). Developed workflow emphasized an in-depth description of each state-of-the-art system/tool, downstream analysis including the authenticity of the taxonomic identity of the transcriptome, global transcriptome map/ network, and functional enrichment of overrepresented genes. The present data-mining approach indicates that bd silkworm mutants are associated with tyrosine (Try) degradation and melanogenesis, which might be mediated by the dopachrome tautomerase (DTC). On the other hand, M. serrata showed overrepresented genes significantly enriched in polyploid-associated functions, including nucleic acid metabolism, intrinsic activity of transposable elements, and functions connected to chloroplasts. Considering all, the present user-friendly workflow helps to identify the molecular evidence for a possible link between the phenome and transcriptome without prior coding knowledge and cost.