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3. Transcriptomics in Plant

Author

Satya, Pratik, Bhattacharjee, Sougata, Sarkar, Debabrata, Roy, Suman, Sharma, Laxmi, Mandal, Nur Alam, Singh, Ram Lakhan, editor, Mondal, Sukanta, editor, Parihar, Akarsh, editor, and Singh, Pradeep Kumar, editor

Published
2022
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10. Pectin biosynthesis pathways are adapted to higher rhamnogalacturonan formation in lignocellulosic jute (Corchorus spp.)

Author

Satya, Pratik, primary, Sarkar, Debabrata, additional, Vijayan, Joshitha, additional, Ray, Soham, additional, Ray, Deb Prasad, additional, Mandal, Nur Alam, additional, Roy, Suman, additional, Sharma, Laxmi, additional, Bera, Amit, additional, Kar, Chandan Sourav, additional, Mitra, Jiban, additional, and Singh, Nagendra Kumar, additional

Published
2020
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11. Genomics for augmenting bast fibre yield and quality improvement in jute

Author

Sarkar, Debabrata, Kundu, Avijit, Avrajit Chakraborty, Mandal, Nur Alam, Debajeet Das, Pratik Satya, Mahato, Ajay Kumar, Pran Gobinda Karmakar, Jiban Mitra, and Nagendra Kumar Singh

Abstract

Jute (Corchorus capsularis L. and C. olitorius L., Malvaceae s. l.) is an important ligno-cellulosic bast fibre crop (2n = 2x = 14), with diversified industrial uses of textiles. We initiated genomics research in jute, with an objective to implement genomics-assisted breeding approaches for bast fibre yield and quality improvement. Here, we present a few important genomic resources and tools made available for jute over the past few years.

Published
2018
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12. Development and validation of SSR and InDel markers in jute (Corchorus olitorius L.) using next-generation sequencing

Author

Mandal, Nur Alam, Avrajit Chakraborty, Tista Basu, Debajeet Das, Kaushlendra Bahadur, Pratik Satya, Pran Gobinda Karmakar, Kar, Chandan Sourav, Jiban Mitra, Paul, Soumitra, Nagendra Kumar Singh, and Debabrata Sarkar

Abstract

We used next-generation sequencing based on Illumina NextSeq (Illumina, San Diego, CA), with 2 x 150 bp chemistry, to assemble de novo the whole genome shotgun (WGS) sequence of Corchorus olitorius cv. Sudan Green and identified genomic SSR and InDel markers. Of 13,814 SSRs identified, the number of di-, tri- and tetra-nucleotide repeat classes were 10,078, 2,388 and 1,348, respectively. Although a total of 5,471 InDels were detected at various positions, we could only identify 44 InDel markers based on stringent parameters. A total of 1,000 SSR (956) and InDel (44) markers were successfully validated in Corchorus spp.

Published
2018
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13. Transcriptome profiling uncovers β-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.)

Author

Satya, Pratik, primary, Chakraborty, Avrajit, additional, Sarkar, Debabrata, additional, Karan, Maya, additional, Das, Debajeet, additional, Mandal, Nur Alam, additional, Saha, Dipnarayan, additional, Datta, Subhojit, additional, Ray, Soham, additional, Kar, Chandan Sourav, additional, Karmakar, Pran Gobinda, additional, Mitra, Jiban, additional, and Singh, Nagendra Kumar, additional

Published
2018
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14. The draft genome of Corchorus olitorius cv. JRO-524 (Navin)

Author

Sarkar, Debabrata, primary, Mahato, Ajay Kumar, additional, Satya, Pratik, additional, Kundu, Avijit, additional, Singh, Sangeeta, additional, Jayaswal, Pawan Kumar, additional, Singh, Akshay, additional, Bahadur, Kaushlendra, additional, Pattnaik, Sasmita, additional, Singh, Nisha, additional, Chakraborty, Avrajit, additional, Mandal, Nur Alam, additional, Das, Debajeet, additional, Basu, Tista, additional, Sevanthi, Amitha Mithra, additional, Saha, Dipnarayan, additional, Datta, Subhojit, additional, Kar, Chandan Sourav, additional, Mitra, Jiban, additional, Datta, Karabi, additional, Karmakar, Pran Gobinda, additional, Sharma, Tilak Raj, additional, Mohapatra, Trilochan, additional, and Singh, Nagendra Kumar, additional

Published
2017
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15. The draft genome of Corchorus olitoriuscv. JRO-524 (Navin)

Author

Sarkar, Debabrata, Mahato, Ajay Kumar, Satya, Pratik, Kundu, Avijit, Singh, Sangeeta, Jayaswal, Pawan Kumar, Singh, Akshay, Bahadur, Kaushlendra, Pattnaik, Sasmita, Singh, Nisha, Chakraborty, Avrajit, Mandal, Nur Alam, Das, Debajeet, Basu, Tista, Sevanthi, Amitha Mithra, Saha, Dipnarayan, Datta, Subhojit, Kar, Chandan Sourav, Mitra, Jiban, Datta, Karabi, Karmakar, Pran Gobinda, Sharma, Tilak Raj, Mohapatra, Trilochan, and Singh, Nagendra Kumar

Abstract

Here, we present the draft genome (377.3Mbp) of Corchorus olitoriouscv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacaofollowed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsyand copiaretrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).

Published
2017
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