Phased secondary small interfering RNAs in Panaxnotoginseng.

Publication Dbxref
PMID:29363419
Structured Abstract Part

  • 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.

Title
Phased secondary small interfering RNAs in Panaxnotoginseng.
Publication Type
Journal Article
Additional Publication Type(s)
Research Support, Non-U.S. Gov't
Series Name
BMC genomics
Volume
19
Publication Year
2018
Issue
Suppl 1
Page Numbers
41
DOI
10.1186/s12864-017-4331-0
Journal Abbreviation
BMC Genomics
EISSN
1471-2164
Publication Date
2018 01 19
Citation
Chen K, Liu L, Zhang X, Yuan Y, Ren S, Guo J, Wang Q, Liao P, Li S, Cui X, Li YF, Zheng Y. Phased secondary small interfering RNAs in Panaxnotoginseng.. BMC genomics. 2018 01 19; 19(Suppl 1):41.
ISSN
1471-2164
Language Abbr
eng
Publication Model
Electronic
Authors
Chen K, Liu L, Zhang X, Yuan Y, Ren S, Guo J, Wang Q, Liao P, Li S, Cui X, Li YF, Zheng Y
Language
English
Elocation
10.1186/s12864-017-4331-0
URL
https://doi.org/10.1186/s12864-017-4331-0
Journal Country
England
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.

Database Reference Annotations
PMID:29363419
Is Obsolete
False
Project
Phased secondary small interfering RNAs in Panax notoginseng