AUTHOR=Saleem Bilal , Farooq Umer , Rehman Obaid Ur , Aqeel Muhammad , Farooq Muhammad Shahbaz , Naeem Muhammad Kashif , Inam Safeena , Ajmal Wajya , Rahim Amna Abdul , Chen Ming , Kalsoom Rabia , Uzair Muhammad , Fiaz Sajid , Attia Kotb , Alafari Hayat Ali , Khan Muhammad Ramzan , Yu Guoping 

TITLE=Genome-wide and molecular characterization of the DNA replication helicase 2 (DNA2) gene family in rice under drought and salt stress

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1039548

DOI=10.3389/fgene.2022.1039548

ISSN=1664-8021

ABSTRACT=<p>Rice plants experience various biotic (such as insect and pest attack) and abiotic (such as drought, salt, heat, and cold <italic>etc.</italic>) stresses during the growing season, resulting in DNA damage and the subsequent losses in rice production. <italic>DNA Replication Helicase</italic>/<italic>Nuclease2 (DNA2)</italic> is known to be involved in DNA replication and repair. In animals and yeast <italic>DNA2</italic> are well characterized because it has the abilities of both helicase and nuclease, it plays a crucial role in DNA replication in the nucleus and mitochondrial genomes. However; they are not fully examined in plants due to less focused on plants damage repair. To fill this research gap, the current study focused on the genome-wide identification and characterization of <italic>OsDNA2</italic> genes, along with analyses of their transcriptional expression, duplication, and phylogeny in rice. Overall, 17 <italic>OsDNA2</italic> members were reported to be found on eight different chromosomes (2, 3, 4, 6, 7, 9, 10, and 11). Among these chromosomes (Chr), Chr4 contained a maximum of six <italic>OsDNA2</italic> genes. Based on phylogenetic analysis, the <italic>OsDNA2</italic> gene members were clustered into three different groups. Furthermore, the conserved domains, gene structures, and <italic>cis</italic>-regulatory elements were systematically investigated. Gene duplication analysis revealed that <italic>OsDNA2_2</italic> had an evolutionary relationship with <italic>OsDNA2_14, OsDNA2_5</italic> with <italic>OsDNA2_6,</italic> and <italic>OsDNA2_1</italic> with <italic>OsDNA2_8.</italic> Moreover, results showed that the conserved domain (AAA_11 superfamily) were present in the <italic>OsDNA2</italic> genes, which belongs to the DEAD-like helicase superfamily. In addition, to understand the post-transcriptional modification of <italic>OsDNA2</italic> genes, miRNAs were predicted, where 653 miRNAs were reported to target 17 <italic>OsDNA2</italic> genes. The results indicated that at the maximum, <italic>OsDNA2_1</italic> and <italic>OsDNA2_4</italic> were targeted by 74 miRNAs each, and <italic>OsDNA2_9</italic> was less targeted (20 miRNAs). The three-dimensional (3D) structures of 17 OsDNA2 proteins were also predicted. Expression of <italic>OsDNA2</italic> members was also carried out under drought and salt stresses, and conclusively their induction indicated the possible involvement of <italic>OsDNA2</italic> in DNA repair under stress when compared with the control. Further studies are recommended to confirm where this study will offer valuable basic data on the functioning of <italic>DNA2</italic> genes in rice and other crop plants.</p>