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Small RNA deep sequencing identifies novel and salt‐stress‐regulated microRNAs from roots of Medicago sativa and Medicago truncatula
Author(s) -
Long RuiCai,
Li MingNa,
Kang JunMei,
Zhang TieJun,
Sun Yan,
Yang QingChuan
Publication year - 2015
Publication title -
physiologia plantarum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.351
H-Index - 146
eISSN - 1399-3054
pISSN - 0031-9317
DOI - 10.1111/ppl.12266
Subject(s) - medicago truncatula , microrna , biology , medicago , small rna , rna , medicago sativa , deep sequencing , abiotic stress , gene , genetics , cdna library , gene expression , computational biology , botany , genome , symbiosis , bacteria
Small 21‐ to 24‐nucleotide (nt) ribonucleic acids ( RNAs ), notably the microRNA ( miRNA ), are emerging as a posttranscriptional regulation mechanism. Salt stress is one of the primary abiotic stresses that cause the crop losses worldwide. In saline lands, root growth and function of plant are determined by the action of environmental salt stress through specific genes that adapt root development to the restrictive condition. To elucidate the role of miRNAs in salt stress regulation in Medicago , we used a high‐throughput sequencing approach to analyze four small RNA libraries from roots of Zhongmu‐1 ( Medicago sativa ) and Jemalong A17 ( Medicago truncatula ), which were treated with 300 m M NaCl for 0 and 8 h. Each library generated about 20 million short sequences and contained predominantly small RNAs of 24‐nt length, followed by 21‐nt and 22‐nt small RNAs . Using sequence analysis, we identified 385 conserved miRNAs from 96 families, along with 68 novel candidate miRNAs . Of all the 68 predicted novel miRNAs , 15 miRNAs were identified to have miRNA *. Statistical analysis on abundance of sequencing read revealed specific miRNA showing contrasting expression patterns between M. sativa and M. truncatula roots, as well as between roots treated for 0 and 8 h. The expression of 10 conserved and novel miRNAs was also quantified by quantitative real‐time reverse transcription polymerase chain reaction ( qRT‐PCR ). The miRNA precursor and target genes were predicted by bioinformatics analysis. We concluded that the salt stress related conserved and novel miRNAs may have a large variety of target mRNAs , some of which might play key roles in salt stress regulation of Medicago .