Test of Small RNA Sequencing Repeatability in Rice
Received date: 2016-04-10
Accepted date: 2016-06-06
Online published: 2016-11-01
Deep sequencing of small RNAs (sRNA) is widely used in sRNAs studies in plants. In order to investigate the sequencing frequency variation of sRNAs, the same sRNA samples from rice grains were sequenced twice using deep sequencing technique. The sRNAs were classified into three categories, high abundance (> 100 RPM), medium abundance (10-100 RPM) and low abundance (1-10 RPM). According to the repeat sequencing data of the same sample, highly expressed sRNAs (> 100 RPM) were less subject to random drift, and 95% of the sRNAs Log2 ratio between two samples fell between -0.649 and 0.558. The same trend was observed in mediumly expressed sRNAs (10-100 RPM), and 95% of the Log2 ratio fell between -0.535 and 0.759. As to lowly expressed sRNAs (1-10 RPM), 95% of the Log2 ratio varied between -1.009 and 1.011. These results can be used as a theoretical guide to find differentially expressed sRNAs in sRNA studies in plants.
Key words： rice; deep sequencing; small RNA; differential expression; random drift
Hong-zheng Sun, Ting Peng, Jing Zhang, Jun-zhou Li, Yan-xiu Du, Quan-zhi Zhao . Test of Small RNA Sequencing Repeatability in Rice[J]. Rice Science, 2017 , 24(1) : 56 -60 . DOI: 10.1016/j.rsci.2016.06.008
| 1 | Altschul S F, Gish W, Miller W, Myers E W, Lipman D J.1990. Basic local alignment search tool.J Mol Biol, 215(3): 403-410. |
| 2 | An F X, Liang Y, Li J F, Chen X L, Han H, Li F H.2014. Construction and significance analysis of the microRNA expression profile of hemerocallis fulva at low temperature.Biosci Biotechnol Biochem, 78(3): 378-383. |
| 3 | Benjamini Y, Yekutieli D.2005. Quantitative trait loci analysis using the false discovery rate. Genetics, 171(2): 783-790. |
| 4 | Bonnet E, van de Peer Y, Rouze P.2006. The small RNA world of plants.New Phytol, 171(3): 451-468. |
| 5 | Brautigam A, Gowik U.2010. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research.Plant Biol (Stuttg), 12(6): 831-841. |
| 6 | Carrington J C, Ambros V.2003. Role of microRNAs in plant and animal development.Science, 301: 336-338. |
| 7 | Cheah B H, Nadarajah K, Divate M D, Wickneswari R.2015. Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage.BMC Genom, 16(1): 692. |
| 8 | Groszmann M, Greaves I K, Albertyn Z I, Scofield G N, Peacock W J, Dennis E S.2011. Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor.Proc Natl Acad Sci USA, 108(6): 2617-2622. |
| 9 | He L, Hannon G J.2004. MicroRNAs: Small RNAs with a big role in gene regulation.Nat Rev Genet, 5(7): 522-531. |
| 10 | Huang J M, Ju Z H, Li Q L, Wang C F, Hou Q L, Li J B, Li R L, Wang L L, Sun T, Hang S Q, Gao Y D, Hou M H, Zhong J F.2011. Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle.Int J Biol Sci, 7(7): 1016-1026. |
| 11 | Khraiwesh B, Arif M A, Seumel G I, Ossowski S, Weigel D, Reski R, Frank W.2010. Transcriptional control of gene expression by microRNAs.Cell, 140(1): 111-122. |
| 12 | Kim V N.2005. Small RNAs: Classification, biogenesis, and function. Mol Cells, 19(1): 1-15. |
| 13 | Kumar R R, Pathak H, Sharma S K, Kala Y K, Nirjal M K, Singh G P, Goswami S, Rai R D.2015. Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.).Funct Integr Genom, 15(3): 323-348. |
| 14 | Liu H, Searle I R., Watson-Haigh N S, Baumann U, Mather D E, Able A J, Able J A.2015. Genome-wide identification of microRNAs in leaves and the developing head of four durum genotypes during water deficit stress.PLoS One, 10(11): e0142799. |
| 15 | Mallory A C, Vaucheret H.2006. Functions of microRNAs and related small RNAs in plants.Nat Genet, 38: S31-836. |
| 16 | Peng T, Lv Q, Zhang J, Li J Z, Du Y X, Zhao Q Z.2011. Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa).J Exp Bot, 62(14): 4943-4954. |
| 17 | Peng T, Sun H Z, Du Y X, Zhang J, Li J Z, Liu Y X, Zhao Y F, Zhao Q Z.2013. Characterization and expression patterns of microRNAs involved in rice grain filling.PLoS One, 8(1): e54148. |
| 18 | Peng T, Sun H Z, Qiao M M, Zhao Y F, Du Y X, Zhang J, Li J Z, Tang G L, Zhao Q Z.2014. Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice.BMC Plant Biol, 14: 196. |
| 19 | Ruiz-Ferrer V, Voinnet O.2009. Roles of plant small RNAs in biotic stress responses.Annu Rev Plant Biol, 60: 485-510. |
| 20 | Secco D, Jabnoune M, Walker H, Shou H X, Wu P, Poirier Y, Whelan J.2013. Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery.Plant Cell, 25(11): 4285-4304. |
| 21 | Voinnet O.2009. Origin, biogenesis, and activity of plant microRNAs.Cell, 136(4): 669-687. |
| 22 | Wang F D, Li H Y, Zhang Y H, Li J J, Li L B, Liu L F, Wang L H, Wang C H, Gao J W.2013. MicroRNA expression analysis of rosette and folding leaves in Chinese cabbage using high-throughput Solexa sequencing.Gene, 532(2): 222-229. |
| 23 | Wang J Y, Yang X D, Xu H B, Chi X Y, Zhang M, Hou X L.2012. Identification and characterization of microRNAs and their target genes in Brassica oleracea.Gene, 505(2): 300-308. |
| 24 | Wu X Y, Ding D, Shi C N, Xue Y D, Zhang Z H, Tang G L, Tang J H.2016. MicroRNA-dependent gene regulatory networks in maize leaf senescence.BMC Plant Biol, 16(1): 73. |
| 25 | Zhao Y T, Wang M, Fu S X, Yang W C, Qi C K, Wang X J.2012. Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production- and development-correlated expression and new small RNA classes.Plant Physiol, 158(2): 813-823. |
| 26 | Zhu F, Wang Z, Sun B Z.2016. Differential expression of microRNAs in shrimp Marsupenaeus japonicus in response to Vibrio alginolyticus infection.Dev Comp Immunol, 55: 76-79. |
| 27 | Zhu Q H, Spriggs A, Matthew L, Fan L J, Kennedy G, Gubler F, Helliwell C.2008. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains.Genom Res, 18(9): 1456-1465. |
/
| 〈 |
|
〉 |