Transcriptome Analysis for Pinus yunnanensis Based on High Throughput Sequencing

doi:10.7525/j.issn.1673-5102.2016.01.011

Abstract

Abstract: The transcriptome of Pinus yunnanensis was sequenced by using Illumina Hiseq 2 000. In total 80 000 Unigene with an average length of 890 nt and N50 of 1 881 nt were obtained by de novo assembly. Of the Unigene, 43 434, 46 415 and 29 418 Unigenes had significant similarity with known data bank in NR, NT and Swiss-Prot, respectively. 14 792 Unigenes were annotated in clusters of orthologous groups of proteins(COG) and assigned to 25 clusters. 26 743 Unigenes were annotated in gene ontology(GO) and grouped into biological processes, cellular components and molecular function three functional categories, 55 sub-categories. The biological processes were most commonly existed. A total of 25 873 Unigenes were divided into 128 Kyoto Encyclopedia of Genes and Genomes(KEGG) pathways whose functions focused on metabolism. We found some Unigenes related to lignin biosynthesis. The sequence data for P.yunnanensis wiill be helpful for the gene discovery and utilization, molecular marker development and genetic improvement in the further research.

Key words: Pinus yunnanensis, transcriptome, Illumina high throughput sequencing technology

CAI Nian-Hui1,2,3；DENG Li-Li1,2,3；XU Yu-Lan1,2,3；XU Yang1,2,3；ZHOU Li1,2,3；WANG Da-Wei1,2,3；TIAN Bin1,2,3；HE Cheng-Zhong1,2,3；DUAN An-An1,2,3. Transcriptome Analysis for Pinus yunnanensis Based on High Throughput Sequencing[J]. Bulletin of Botanical Research, 2016, 36(1): 75-83.

References

1.金振洲,彭鉴.云南松［M］.昆明:云南科技出版社,2004:1-66.

2.中国科学院昆明植物研究所编著.云南植物志(第4卷):种子植物［M］.北京:科学出版社,1986:54-57.

3.中国科学院中国植物志编辑委员会.中国植物志:第7卷［M］.北京:科学出版社,1978:122-282.

4.陈飞,王健敏,孙宝刚,等.云南松的地理分布与气候关系［J］.林业科学研究,2012,25(2):163-168.

5.陈飞,王健敏,陈晓鸣,等.基于Kira指标的云南松气候适宜性分析［J］.林业科学研究,2012,25(5):576-581.

6.邓喜庆,皇宝林,温庆忠,等.云南松林资源动态研究［J］.自然资源学报,2014,29(8):1411-1419.

7.邓喜庆,皇宝林,温庆忠,等.云南松林在云南的分布研究［J］.云南大学学报:自然科学版,2013,35(6):843-848.

8.Zhang L,Xu W H,Ouyang Z Y,et al.Determination of priority nature conservation areas and human disturbances in the Yangtze River Basin,China［J］.Journal for Nature Conservation,2014,22(4):326-336.

9.Xiao X Y,Haberle S G,Shen J,et al.Latest Pleistocene and Holocene vegetation and climate history inferred from an alpine lacustrine record,northwestern Yunnan Province,southwestern China［J］.Quaternary Science Reviews,2014,86(2):35-48.

10.Wu J X,Wang Y X,Chen Q B,et al.Soil improvement of Pinus yunnanensis forest at different age in Central Yunnan Plateau［J］.Advanced Materials Research,2014,864-867:2565-2568.

11.Lin Y M,Cui P,Ge Y G,et al.The succession characteristics of soil erosion during different vegetation succession stages in dry-hot river valley of Jinsha River,upper reaches of Yangtze River［J］.Ecological Engineering,2014,62(1):13-26.

12.Wang B S,Mao J F,Zhao W,et al.Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis［J］.PLoS ONE,2013,8(6):e67345.

13.Xu Y L,Zhang R L,Tian B,et al.Development of novel microsatellite markers for Pinus yunnanensis and their cross amplification in congeneric species［J］.Conservation Genetics Resources,2013,5(4):1113-1114.

14.Li X,Yang X,Wu H X.Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism［J］.BMC Genomics,2013,14(22):547-554.

15.Niu S H,Li Z X,Yuan H W,et al.Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny［J］.BMC Genomics,2013,14(1):202-207.

16.Pinosio S,González-Martínez S C,Bagnoli F,et al.First insights into the transcriptome and development of new genomic tools of a widespread circum-mediterranean tree species,Pinus halepensis Mill.［J］.Molecular Ecology Resources,2014,14(4):846-856.

17.Wan L C,Zhang H,Lu S,et al.Transcriptome-wide identification and characterization of mirnas from Pinus densata［J］.BMC Genomics,2012,13(1):132-142.

18.Fang P,Niu S,Yuan H,et al.Development and characterization of 25 EST-SSR markers in Pinus sylvestris var.mongolica(Pinaceae)［J］.Applications in Plant Sciences,2014,2(1):1300057.

19.Feng Y H,Yang Z Q,Wang J,et al.Development and characterization of SSR markers from Pinus massoniana and their transferability to P.elliottii,P.caribaea and P.yunnanensis［J］.Genetics & Molecular Research Gmr,2014,13(1):1508-1513.

20.Iwaizumi M G,Tsuda Y,Ohtani M,et al.Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan［J］.Forest Ecology & Management,2013,304(4):407-416.

21.Lesser M R,Parchman T L,Buerkle C.Cross-species transferability of SSR loci developed from transciptome sequencing in lodgepole pine［J］.Molecular Ecology Resources,2012,12(3):448-455.

22.Liu J J,Hammett C.Development of novel polymorphic microsatellite markers by technology of next generation sequencing in western white pine［J］.Conservation Genetics Resources,2014,6(3):647-648.

23.Conesa ,Götz S,García-Gómez J M,et al.Blast2GO:A universal tool for annotation,visualization and analysis in functional genomics research［J］.Bioinformatics,2005,21(18):3674-3676.

24.Ye J,Fang L,Zheng H,et al.WEGO:a web tool for plotting GO annotations［J］.Nucleic Acids Research,2006,34(2):293-297.

25.Tatusov R L,Galperln M Y,Natale D A,et al.The COG database:A tool for genome-scale analysis of protein functions and evolution［J］.Nucleic Acids Research,2000,28(1):33-36.

26.Kanehisa M,Goto S,Kawashima S,et al.The KEGG resource for deciphering the genome［J］.Nucleic Acids Research,2004,32(22):277-280.

27.Zimin A,Stevens K A,Crepeau M W,et al.Sequencing and assembly of the 22-gb loblolly pine genome［J］.Genetics,2014,196(3):875-890.

28.王晓峰,何怀卫龙,蔡卫佳,等.马尾松转录组测序和分析［J］.分子植物育种,2013,11(3):385-392.

29.Bai T D,Xu L,Xu M,et al.Characterization of masson pine(Pinus massoniana Lamb.) microsatellite DNA by 454 genome shotgun sequencing［J］.Tree Genetics & Genomes,2014,10(2):429-437.

30.郑纪伟.柳树转录组高通量测序及SSR标记开发研究［D］.南京:南京林业大学,2013.

31.邓敏捷,董焱鹏,赵振利,等.基于Illumina高通量测序的泡桐转录组研究［J］.林业科学,2013,49(6):30-36.

32.刘玉林,李伟,张志翔.基于高通量测序的辽东栎转录组学研究［J］.生物技术通报,2014(7):119-124.

33.张琳,范晓明,林青,等.锥栗种仁转录组及淀粉和蔗糖代谢相关酶基因的表达分析［J］.植物遗传资源学报,2015,16(3):603-612.

[1]	Zhanmin ZHENG, Yubing SHANG, Guangbo ZHOU, Di XIAO, Yi LIU, Xiangling YOU. Genetic Transformation and Function Analysis of PsnHB13 and PsnHB15 of Populus simonii × Populus nigra [J]. Bulletin of Botanical Research, 2023, 43(3): 340-350.
[2]	Dongmei HUANG, Ying CHEN, Lu BAI, Di’an NI, Yiyang XU, Zhiguo ZHANG, Qiaoping QIN. Transcriptome Analysis of Hemerocallis fulva Leaves Respond to Low Temperature Stress [J]. Bulletin of Botanical Research, 2022, 42(3): 424-436.
[3]	Jingya Yu, Mingze Xia, Hao Xu, Faqi Zhang. Comparative Transcriptome Analysis of Three Artemisia Species in Qinghai Tibet Plateau [J]. Bulletin of Botanical Research, 2022, 42(2): 200-210.
[4]	Xue-Yan ZHAO, Si-Feng LI, Guo-Qing BAI, Wei-Min LI. Comparative Transcriptome Analysis of Five Species of Lilium [J]. Bulletin of Botanical Research, 2021, 41(4): 614-625.
[5]	Yun TENG, Zong-Bo QIU, Wen-Li WANG, Xue-Ru ZHANG. Transcriptome Analysis in Vascular Cambium and Xylem of Paulownia tomentosa [J]. Bulletin of Botanical Research, 2021, 41(3): 354-361.
[6]	Chen-Chen ZHOU, Yi-Liang LI, Zhe WANG, Fen-Cheng ZHAO, Sui-Ying ZHONG, Chang-Ming LIN, Zhi-Qiang TAN, Fu-Ming LI, Hui-Shan WU, Wen-Bing GUO, Fang-Yan LIAO, Jian-Ge WANG. Screening and Expression Analysis of Different Genes for Oleoresin Production in the Specific Period of Pinus elliottii×P.caribaea by RNA-Seq Technology [J]. Bulletin of Botanical Research, 2021, 41(3): 419-428.
[7]	Lin LU, Shang-Yu YANG, Wei-Dong LIU, Li-Ming LU. To Explore the Transcription Factor in Response to Low Temperature Stress in Nicotiana alata by Transcriptome Sequencing [J]. Bulletin of Botanical Research, 2021, 41(1): 119-129.
[8]	Li-Qiang ZHAO, Chun-Miao SHAN, Sheng-Xiang ZHANG, Yuan-Yuan SHI, Ke-Long MA, Jia-Wen WU. Identification of Key Enzyme Genes Involved in Anthocyanin Synthesis pathway in Clinopodium gracile by Transcriptome Analysis [J]. Bulletin of Botanical Research, 2020, 40(6): 886-896.
[9]	LIU Dan, ZENG Qin-Meng, LIU Bin, LI Yu, CHEN Shi-Pin. Transcriptome Analysis and Gene Functional Annotation in Phoebe bournei [J]. Bulletin of Botanical Research, 2020, 40(4): 613-622.
[10]	ZHANG Yu, XIA Ming-Ze, ZHANG Fa-Qi. Transcriptome Analysis for Medicinal Plant Anisodus tanguticus [J]. Bulletin of Botanical Research, 2020, 40(3): 458-467.
[11]	ZHU Li-Li, DU Qing-Xin, HE Feng, QING Jun, DU Hong-Yan. Sequencing Analysis of Transcriptome of Male Floral Bud at Two Development Stages in Eucommia ulmoides [J]. Bulletin of Botanical Research, 2020, 40(2): 284-292.
[12]	YE Xing-Zhuang, LIU Dan, LUO Jia-Jia, FAN Hui-Hua, ZHANG Guo-Fang, LIU Bao, CHEN Shi-Pin. Transcriptome Analysis for Rare and Endangered Plants of Semiliquidambar cathayensis [J]. Bulletin of Botanical Research, 2019, 39(2): 276-286.
[13]	LIU Xiong-Fang, LI Tai-Qiang, ZHANG Xu, LI Zheng-Hong, WAN You-Ming, AN Jing, LIU Xiu-Xian, MA Hong. Characteristic Analysis of Microsatellites in the Transcriptome of Phyllanthus emblica,an Important Edible and Medicinal Plant [J]. Bulletin of Botanical Research, 2019, 39(2): 294-302.
[14]	WANG Da-Wei, ZHOU Fan, SHEN Bing-Qi, WANG Lian-Chun. Characteristics of Microsatellite in Camellia saluenensis by High-throughput Sequencing [J]. Bulletin of Botanical Research, 2019, 39(1): 148-155.
[15]	LI Yan, GENGJI Zhuo-Ma, JIA Liu-Kun, WANG Zhi-Hua, CHEN Shi-Long, GAO Qing-Bo. Analysis of SSR Information in Transcriptome Sequences of Saxifraga sinomontana [J]. Bulletin of Botanical Research, 2018, 38(6): 939-947.