Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD

Shi, Pei Yong; Wu, Tao; Li, Panpan; Guo, Bingjie; Fang, Gang; Dong, Yafei

doi:10.1049/iet-syb.2016.0043

Cited by 2 publications

(2 citation statements)

References 23 publications

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“…PlasMapper generates plasmid maps along with annotations. It provides multiple predictions, such as replication origin, promotor, terminator, selectable marker, regulatory sequence affinity tag, miscellaneous feature, report gene, and restriction site predictions ( Shi et al, 2017 ). The Vigna umbellate draft assembly was subjected to identify these elements to report additional genome-editing scaled tools.…”

Section: Methodsmentioning

confidence: 99%

De novo genome assembly of rice bean (Vigna umbellata) – A nominated nutritionally rich future crop reveals novel insights into flowering potential, habit, and palatability centric – traits for efficient domestication

et al. 2022

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Rice bean is a less-known underutilized legume crop with a high nutritional value among members of the Vigna family. As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimated identification of 31,276 high confidence index genes via 15,521 scaffolds generated from Illumina and PacBio platform 30X coverage data has achieved 96.08% functional coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to Vigna angularis (experimental control/outgroup), Vigna radiata, and Vigna unguiculata, however, Vigna angularis being the closest. The assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete coding sequence (CDS) alignment. In contrast, 17 medically influential genomes from the National Institute of General Medical Sciences-National Institutes of Health NIGMS-NIH, when compared to rice bean assembly for LCB clusters, led to the identification of more than 18,000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Significantly, we found deserving late-flowering genes, palatably indexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Therefore, the findings from this report address the genomic value of rice bean to be escalated via breeding by allied and applied approaches.

show abstract

Section: Methodsmentioning

confidence: 99%

De novo genome assembly of rice bean (Vigna umbellata) – A nominated nutritionally rich future crop reveals novel insights into flowering potential, habit, and palatability centric – traits for efficient domestication

et al. 2022

View full text Add to dashboard Cite

show abstract

“…PlasMapper generates plasmid maps along with annotations. It provides multiple predictions, such as replication origin, promotor, terminator, selectable marker, regulatory sequence affinity tag, miscellaneous feature, report gene and restriction site predictions (Shi et al, 2017). The Vigna umbellata draft assembly was subjected to identify these elements to report additional genome-editing scaled tools.…”

Section: Distributionsmentioning

confidence: 99%

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop

Kaul

Eswaran

Thangaraj

et al. 2019

Preprint

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Rice bean is a less well known and underutilized legume crop that has proved to be highly favourable due to its rich nutritional value in comparison with other members of the Vigna family. As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimate of 31276 highly confidential genes from 15521 scaffolds and functional coverage of 96.08% was sequenced from 30X coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to V. angularis (experimental control/outgroup), V. radiata and V. unguiculata, however, V. angularis being the closest. Heuristically, the assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete CDS alignment. In contrast, 17 medically influential genomes from NIGMS-NIH, when compared with rice bean assembly for LCB clusters led to identification of more than 18000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Signifiacantly, we found deserving late-flowering genes, palatablyindexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Further, we developed a repository for underutilised crop genome facility using D3.js at www.nicg.in. Therefore, the findings from this report addresses the genomic value of rice bean to be escalated via breeding by allied and applied approaches.Research), IBPR (International Board for Plant Genetic Resources) and ICUC (International Centre for Underutilized Crops) organisations, form a network called FOSRIN (Food Security through Ricebean Research in India and Nepal), wherein Rice bean has been labeled as one of the future crops foreseen for domestication by farmers in marginal lands (Venkatesha 2012).Despite the nutritional excellence of rice bean, the prevailing lack of awareness of its complete nutritional benefits means that rice bean can be categorized as an underutilized crop. Rice bean can become established and grow in various soil types. It is pest resistant and presents tremendous potential as a nutritious fodder and high-quality grain. The major drawbacks of this pulse crop of the kharif season include late flowering, indeterminate nature and tastelessness. Furthermore, there are meagre possibilities for the improvement of rice bean due to its predominant landraces, nominal modern plant breeding and limited seed supply. Consequently, the high diversity retained within its limited geographical distribution and the existence of few marketing channels mean that there is a great scope for the genetic improvement of rice bean. Despite the importance of rice bean as a multipurpose legume utilized for culinary purpos...

show abstract

Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD

Cited by 2 publications

References 23 publications

De novo genome assembly of rice bean (Vigna umbellata) – A nominated nutritionally rich future crop reveals novel insights into flowering potential, habit, and palatability centric – traits for efficient domestication

De novo genome assembly of rice bean (Vigna umbellata) – A nominated nutritionally rich future crop reveals novel insights into flowering potential, habit, and palatability centric – traits for efficient domestication

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop

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