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Phased secondary small interfering RNAs in Panaxnotoginseng

Authors :
Kun Chen
Li Liu
Xiaotuo Zhang
Yuanyuan Yuan
Shuchao Ren
Junqiang Guo
Qingyi Wang
Peiran Liao
Shipeng Li
Xiuming Cui
Yong-Fang Li
Yun Zheng
Source :
BMC Genomics, Vol 19, Iss S1, Pp 57-66 (2018)
Publication Year :
2018
Publisher :
BMC, 2018.

Abstract

Abstract Background Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Methods Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5’-RACE to validate some of the identified phasiRNA targets. Results After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs, respectively, were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5’-RACE analysis. We also found that miR171 with 21 nt triggers the generations of 21 nt phasiRNAs from its conserved targets. Conclusions We validated that some phasiRNAs generated from PPRs and TASL genes are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.

Details

Language :
English
ISSN :
14712164
Volume :
19
Issue :
S1
Database :
Directory of Open Access Journals
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
edsdoj.53b00aa441c146e69756e9de3d5f4d3b
Document Type :
article
Full Text :
https://doi.org/10.1186/s12864-017-4331-0