Ahmed Milad, Ahmed Foeaz, Ahmed Jamil, Akhand Mst Rubaiat Nazneen, Azim Kazi Faizul, Imran Md Abdus Shukur, Hoque Syeda Farjana, Hasan Mahmudul
Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
Heliyon. 2021 Apr 8;7(4):e06705. doi: 10.1016/j.heliyon.2021.e06705. eCollection 2021 Apr.
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 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.
黄麻在天然纤维生产中占据主导地位，且对环境威胁较小。长度约为21至24个核苷酸的小型非编码微小RNA在调节基因表达以及细胞生长和发育的不同功能中发挥着重要作用。在此，该研究采用了一种全面的计算机模拟方法，以鉴定和表征黄麻基因组中的保守微小RNA，包括特定基因靶标的功能注释。基于表达序列标签（EST）对双子叶植物的3350个已知微小RNA与黄麻基因组的763个非冗余EST进行同源性搜索，预测出属于五个不同微小RNA家族（miR1536、miR9567-3p、miR4391、miR11300和miR8689）的5个潜在微小RNA候选物。推定的微小RNA由18个核苷酸组成，其前体微小RNA的最小自由能指数（MFEI）值范围为-0.49至-1.56，（A + U）含量为55%-61%。共鉴定出推定微小RNA的1052个基因靶标，并对其功能进行了广泛分析。大多数基因靶标参与植物生长、细胞周期调控、细胞器合成、发育过程和环境响应。发现五个基因靶标，即含NAC结构域蛋白、WRKY DNA结合蛋白、3-脱氢奎尼酸合酶、S-腺苷-L-甲硫氨酸依赖性甲基转移酶和血管相关NAC结构域，参与木质素生物合成、苯丙烷途径和次生壁形成。本研究可能会加速更多微小RNA的发现，加强对微小RNA在木质素生物合成细胞基础中关联的全面理解，以生产高标准的黄麻产品。
