Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Abstract Background MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwi...
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doaj-37533a2542ea4c5a94a5f31cf13f57c32020-11-24T21:12:13ZengBMCBMC Genomics1471-21642018-05-0119S2617210.1186/s12864-018-4457-8Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelonLi Liu0Shuchao Ren1Junqiang Guo2Qingyi Wang3Xiaotuo Zhang4Peiran Liao5Shipeng Li6Ramanjulu Sunkar7Yun Zheng8Faculty of Life Science and Technology, Kunming University of Science and TechnologyFaculty of Life Science and Technology, Kunming University of Science and TechnologyFaculty of Information Engineering and Automation, Kunming University of Science and TechnologyFaculty of Information Engineering and Automation, Kunming University of Science and TechnologySchool of Life Sciences, Fudan UniversityFaculty of Life Science and Technology, Kunming University of Science and TechnologyFaculty of Life Science and Technology, Kunming University of Science and TechnologyDepartment of Biochemistry and Molecular Biology, Oklahoma State UniversityYunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyAbstract Background MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. However, the watermelon miRNAs and phasiRNAs and their functions are not well explored. Results Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, petals, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed using the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 127 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. Conclusions The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.http://link.springer.com/article/10.1186/s12864-018-4457-8Citrullus lanatus L.High-throughput sequencingmicroRNAPHASPhased small interfering RNA (phasiRNA)Bioinformatics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Li Liu Shuchao Ren Junqiang Guo Qingyi Wang Xiaotuo Zhang Peiran Liao Shipeng Li Ramanjulu Sunkar Yun Zheng |
spellingShingle |
Li Liu Shuchao Ren Junqiang Guo Qingyi Wang Xiaotuo Zhang Peiran Liao Shipeng Li Ramanjulu Sunkar Yun Zheng Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon BMC Genomics Citrullus lanatus L. High-throughput sequencing microRNA PHAS Phased small interfering RNA (phasiRNA) Bioinformatics |
author_facet |
Li Liu Shuchao Ren Junqiang Guo Qingyi Wang Xiaotuo Zhang Peiran Liao Shipeng Li Ramanjulu Sunkar Yun Zheng |
author_sort |
Li Liu |
title |
Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon |
title_short |
Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon |
title_full |
Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon |
title_fullStr |
Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon |
title_full_unstemmed |
Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon |
title_sort |
genome-wide identification and comprehensive analysis of micrornas and phased small interfering rnas in watermelon |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-05-01 |
description |
Abstract Background MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. However, the watermelon miRNAs and phasiRNAs and their functions are not well explored. Results Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, petals, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed using the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 127 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. Conclusions The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon. |
topic |
Citrullus lanatus L. High-throughput sequencing microRNA PHAS Phased small interfering RNA (phasiRNA) Bioinformatics |
url |
http://link.springer.com/article/10.1186/s12864-018-4457-8 |
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