Browsing by Author "Yadav, Manju"

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    A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)
    (John Wiley & Sons, 2013) Jain, Mukesh; Misra, Gopal; Patel, Ravi K.; Priya, Pushp; Jhanwar, Shalu; Khan, Aamir W.; Shah, Niraj; Singh, Vikas K.; Garg, Rohini; Jeena, Ganga; Yadav, Manju; Kant, Chandra; Sharma, Priyanka; Yadav, Gitanjali; Bhatia, Sabhyata; Tyagi, Akhilesh K.; Chattopadhyay, Debasis
    Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi-type chickpea genome using next-generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520-Mb assembly covers 70% of the predicted 740-Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27,571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole-genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties.
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    Patterns of codon usage in plastidial genomes of ancient plants provide insights into evolution
    (2015) Yadav, Manju; Babu, Suresh; Yadav, Gitanjali
    Basal angiosperms are the first flowering plants that diverged from ancestral angiosperms, while magnoliids represent the oldest known angiosperms and are considered to retain the characteristics of more primitive angiosperms. Availability of the plastidial genomes from several members of both these classes of plants provides an opportunity to identify and understand large-scale genomic patterns in organelles of early angiosperms. In this work, chloroplast genomes from nine AT-rich basal angiosperm and magnoliid species were analyzed to unearth patterns, if any, in terms of codon bias and to identify factors responsible for the detected patterns. We were able to distinguish nine optimal codons in basal angiosperm chloroplasts and 18 in case of magnoliids. Our findings suggest mutational bias as the most predominant factor shaping codon usage patterns among the genomes examined, while gene expression, hydrophobicity and aromaticity, were found to have a limited but important effect on pattern determination.