Identification and characterization of conserved and novel microRNAs in Xanthoceras sorbifolium via deep sequencing

다국어 초록 (Multilingual Abstract)

Xanthoceras sorbifolium is an economicallyimportant woody plant in China. Plant microRNAs (miRNAs)play a vital role in plant development. We usedSolexa technology to sequence a small RNA library fromthe buds, young and mature leaves, flowers, and developingseeds (10, 30, and 60 days after pollination) of X. sorbifoliumto identify conserved and novel miRNAs. Sequenceanalysis identified 49 conserved miRNAs belonging to 19miRNA families, as well as four novel miRNAs. An analysisof 10 miRNA sequences by qRT-PCR showed that allsequences were expressed and that they were dynamicallyregulated in different tissues. Finally, seven targets of thenovel miRNAs were predicted. This study opens up a newavenue for understanding the roles of miRNAs in X.
sorbifolium.

참고문헌 (Reference)

1 Maute RL, "tRNA-derived microRNA modulates proliferation and the DNA damage response and is downregulated in B cell lymphoma" 110 : 1404-1409, 2013

2 Dai X, "psRNATarget: a plant small RNA target analysis server" 39 : 155-159, 2011

3 Liu Y, "Transcriptome analysis of yellow horn (Xanthoceras sorbifolium Bunge): a potential oilrich seed tree for biodiesel in China" 8 : e74441-, 2013

4 Lippman Z, "The role of RNA interference in heterochromatic silencing" 431 : 364-370, 2004

5 Keam SP, "The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells" 42 : 8984-8995, 2014

6 Gottesman S, "The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system" 12 : 1338-1347, 1998

7 Lu S, "Stress-responsive microRNAs in Populus" 55 : 131-151, 2008

8 Xing S, "SPL8 and miR156-targeted SPL genes redundantly regulate Arabidopsis gynoecium differential patterning" 75 : 566-577, 2013

9 Li R, "SOAP: short oligonucleotide alignment program" 24 : 713-714, 2008

10 Carrington JC, "Role of microRNAs in plant and animal development" 301 : 336-338, 2003

11 Yu HY, "Preparation of biodiesel from Xanthoceras sorblfolia Bunge seed oil" 34 : 43-45, 2009

12 Sunkar R, "Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis" 16 : 2001-2019, 2004

13 Lu S, "Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis" 17 : 2186-2203, 2005

14 Bartel DP, "MicroRNAs: genomics, biogenesis, mechanism, and function" 116 : 281-297, 2004

15 Lu S, "MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development" 51 : 1077-1098, 2007

16 Jones-Rhoades MW, "MicroRNAs and their regulatory roles in plants" 57 : 19-53, 2006

17 Zhao M, "Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis" 190 : 906-915, 2011

18 Pant BD, "Identification of nutrient-responsive Arabidopsis and rapeseed MicroRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing" 150 : 1541-1555, 2009

19 Pantaleo V, "Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis" 62 : 960-976, 2010

20 Yu X, "Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa" 63 : 1025-1038, 2011

21 Puzey JR, "Identification of conserved Aquilegia coerulea microRNAs and their targets" 448 : 46-56, 2009

22 Yan Ao, "Identification and comparative profiling of microRNAs in wild-type Xanthoceras sorbifolia and its double flower mutant" 한국유전학회 34 (34): 561-568, 2012

23 Barrera-Figueroa BE, "Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes" 11 : 127-, 2011

24 Allen RS, "Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family" 104 : 16371-16376, 2007

25 Kwak P, "Enrichment of a set of microRNAs during the cotton fiber development" 10 : 457-, 2009

26 Lu C, "Elucidation of the small RNA component of the transcriptome" 309 : 1567-1569, 2005

27 Zhang J, "Dynamic expression of small RNA populations in larch (Larix leptolepis)" 237 : 89-101, 2013

28 Kwon C, "Detection of PIWI and piRNAs in the mitochondria of mammalian cancer cells" 446 : 218-223, 2014

29 Wei LQ, "Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa" 12 : R53-, 2011

30 Zhang J, "Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response" 10 : 449-, 2009

31 Zhao C-Z, "Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.)" 10 : 3-, 2010

32 Meyers BC, "Criteria for annotation of plant MicroRNAs" 20 : 3186-3190, 2008

33 Stief A, "Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors" 26 : 1792-1807, 2014

34 Gao SM, "Advances in research on Xanthoceras sorbifolium" 19 : 296-301, 2002

35 Chang S, "A simple and efficient method for isolating RNA from pine trees" 11 : 113-116, 1993