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Sequencing and de novo transcriptome assembly for discovering regulators of gene expression in Jack (Artocarpus heterophyllus)

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Title Sequencing and de novo transcriptome assembly for discovering regulators of gene expression in Jack (Artocarpus heterophyllus)
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Creator Tribhuvan Kishor U.
Singh Devendra K.
Pradhan Bhubaneshwar
Bishi Sujit K.
Pandey Avinash
Kumar Sudhir
Bhati Jyotika
Mishra Dwijesh C
Das Antra
Sharma T.R.
Pattanayak A.
Singh Binay K.
 
Subject Artocarpus heterophyllus
Transcriptome assembly
lncRNA
eTM
Transcription regulators
 
Description Not Available
Jack (Artocarpus heterophyllus) is a multipurpose fruit-tree species with minimal genomic resources. The study reports developing comprehensive transcriptome data containing 80,411 unigenes with an N50 value of 1265 bp. We predicted 64,215 CDSs from the unigenes and annotated and functionally categorized them into the biological process (23,230), molecular function (27,149), and cellular components (17,284). From 80,411 unigenes, we discovered 16,853 perfect SSRs with 192 distinct repeat motif types reiterating 4 to 22 times. Besides, we identified 2741 TFs from 69 TF families, 53 miRNAs from 19 conserved miRNA families, 25,953 potential lncRNAs, and placed three functional eTMs in different lncRNA-miRNA pairs. The regulatory networks involving genes, TFs, and miRNAs identified several regulatory and regulated nodes providing insight into miRNAs' gene associations and transcription factor-mediated regulation. The comparison of expression patterns of some selected miRNAs vis-à-vis their corresponding target genes showed an inverse relationship indicating the possible miRNA-mediated regulation of the genes.
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Date 2022-04-19T08:05:47Z
2022-04-19T08:05:47Z
2022-05-01
 
Type Research Paper
 
Identifier Kishor U. Tribhuvan, Devendra K. Singh, Bhubaneshwar Pradhan, Sujit K. Bishi, Avinash Pandey, Sudhir Kumar, Jyotika Bhati, Dwijesh C. Mishra, Antra Das, T.R. Sharma, A. Pattanayak, Binay K. Singh (2022). Sequencing and de novo transcriptome assembly for discovering regulators of gene expression in Jack (Artocarpus heterophyllus), Genomics, 114(3), 110356.
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http://krishi.icar.gov.in/jspui/handle/123456789/71630
 
Language English
 
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Publisher Not Available