Sex specific expression and distribution of small RNAs in papaya

BMC Genomics

Research Article

Guru Jagadeeswaran¹  Ramanjulu Sunkar¹  Rishi Aryal²  Ray Ming³  Qingyi Yu⁴  Yun Zheng⁵ 

[1] Department of Biochemistry and Molecular Biology, Oklahoma State University, 74078, Stillwater, OK, USA;Department of Plant Biology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA;Department of Plant Biology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA;FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China;Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research Center, Texas A&M University System, 75252, Dallas, TX, USA;FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China;Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China;

关键词: Carica papaya;    Centromere;    miRNA;    siRNA;    Sex chromosome;    Sex determination;   

DOI  :  10.1186/1471-2164-15-20

 received in 2013-10-03, accepted in 2013-12-30,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundRegulatory function of small non-coding RNAs (sRNA) in response to environmental and developmental cues has been established. Additionally, sRNA, also plays an important role in maintaining the heterochromatin and centromere structures of the chromosome. Papaya, a trioecious species with recently evolved sex chromosomes, has emerged as an excellent model system to study sex determination and sex chromosome evolution in plants. However, role of small RNA in papaya sex determination is yet to be explored.ResultsWe analyzed the high throughput sRNAs reads in the Illumina libraries prepared from male, female, and hermaphrodite flowers of papaya. Using the sRNA reads, we identified 29 miRNAs that were not previously reported from papaya. Including this and two previous studies, a total of 90 miRNAs has been identified in papaya. We analyzed the expression of these miRNAs in each sex types. A total of 65 miRNAs, including 31 conserved and 34 novel mirNA, were detected in at least one library. Fourteen of the 65 miRNAs were differentially expressed among different sex types. Most of the miRNA expressed higher in male flowers were related to the auxin signaling pathways, whereas the miRNAs expressed higher in female flowers were the potential regulators of the apical meristem identity genes. Aligning the sRNA reads identified the sRNA hotspots adjacent to the gaps of the X and Y chromosomes. The X and Y chromosomes sRNA hotspots has a 7.8 and 4.4 folds higher expression of sRNA, respectively, relative to the chromosome wide average. Approximately 75% of the reads aligned to the X chromosome hotspot was identical to that of the Y chromosome hotspot.ConclusionBy analyzing the large-scale sRNA sequences from three sex types, we identified the sRNA hotspots flanking the gaps of papaya X, Y, and Yh chromosome. The sRNAs expression patterns in these regions were reminiscent of the pericentromeric region indicating that the only remaining gap in each of these chromosomes is likely the centromere. We also identified 14 differentially expressed miRNAs in male, female and hermaphrodite flowers of papaya. Our results provide valuable information toward understanding the papaya sex determination.

【 授权许可】

Unknown   
© Aryal et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.