In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis

Milad Ahmed; Foeaz Ahmed; Jamil Ahmed; Mst Rubaiat Nazneen Akhand; Kazi Faizul Azim; Md Abdus Shukur Imran; Syeda Farjana Hoque; Mahmudul Hasan

doi:10.1016/j.heliyon.2021.e06705

In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis

Heliyon. 2021 Apr 8;7(4):e06705. doi: 10.1016/j.heliyon.2021.e06705. eCollection 2021 Apr.

Authors

Milad Ahmed^{1

2}, Foeaz Ahmed^{1

3}, Jamil Ahmed^{1

4}, Mst Rubaiat Nazneen Akhand^{1

4}, Kazi Faizul Azim^{1

5}, Md Abdus Shukur Imran^{1

6}, Syeda Farjana Hoque^{1

6}, Mahmudul Hasan^{1

6}

Affiliations

¹ Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
² Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
³ Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
⁴ Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
⁵ Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
⁶ Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.

Abstract

Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre alongside lower environmental threat. Small noncoding ~21 to 24 nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including functional annotation of specific gene targets. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome, resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were composed of 18 nucleotides having a range of -0.49 to -1.56 MFEI values and 55%-61% of (A + U) content in their pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. Five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met-dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation. The present study might accelerate the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

Keywords: Corchorus capsularis; ESTs; Jute; Lignin; MicroRNA; Natural fibre.