柳杉维管形成层及木质部区转录组序列及基因表达分析
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摘要
柳杉是中国南方重要的针叶用材树种,具有树形高大,纹理直等特点,已广泛用于板材和建筑生产中,研究柳杉木材形成过程中维管形成层及木质部区转录组特征,为木材形成主要过程的分子机理,木材形成有关基因调控,培育优良材质的林木提供理论参考。本研究以柳杉形成层组织为材料,通过Illumina Hiseq测序平台对4个不同发育阶段的柳杉维管形成层进行转录组测序;对Unigene进行了蛋白功能注释、分类及KEGG代谢通路分析等。测序数据参照无参转录组测序流程进行分析,一共产生105.9 Gb的数据,过滤后Clean reads均达到90%以上。Clean reads经Trinity软件进行组装,一共产生64 969个Unigene,对Unigene进行拼接,拼接后的Contigs序列有29 381条、Singletons有35 588条,总长度为83 003 836 bp。将Unigen与七大功能数据库(NR, NT, GO, COG, KEGG, Swissprot, Interpro)进行比对,共有42 836个Unigene得到注释,占总Unigene的66.05%。GO注释共有89 644个转录本得到注释。对GO注释转录本进行分类,其中有38 432个转录本(42.87%)注释为生物过程,有32 749个转录本(36.53%)注释为细胞组分,有18 463个转录本(20.6%)注释为分子功能。KEGG注释有31 580个Unigene得到注释。分为6大类为:细胞代谢过程、环境信息处理、遗传信息处理、人类疾病、代谢作用、生物体系统。其中代谢作用涉及的Unigene最多达18 580个,占KEGG总注释Unigene的58.83%。另有37 762个Unigene得到COG注释,被分为25类,其中注释数目最多的类型是仅预测一般功能的Unigene,占总数的16.9%;其次是转录,比例为8.8%;再次是复制、重组及修复,占总数的7.8%。本研究最后分析了可能参与木材形成重要功能基因,为探讨木材发育的分子机制及进行重要功能基因的挖掘提供了提供了依据。
Cryptomeria fortunei is an important coniferous timber tree in southern China, which has the characteristics of tall shape and straight texture. It has been widely used in plate and building material production. The characteristics of the transcriptome of vascular cambium and xylem zone were studied and analyzed, which would lay a theoretical basis for further study of the molecular mechanism and genetic regulation during the process of wood formation, and the cultivation of fine woods. In this study, cambium tissue of C. fortunei was used as test materials,and the transcriptome sequencing of C. fortunei vascular cambium at four different development stages was conducted based on Illumina Hiseq sequencing platform. The protein functional annotation, GO classification and KEGG metabolic pathway analysis of Unigene were performed. The sequencing data were analyzed according to the procedure of no-reference transcriptome sequencing. A total of 105.9 Gb data were obtained and the filtered clean reads reached more than 90%. Clean reads were assembled by Trinity software and a total of 64 969 Unigenes(29 381 contigs and 35 588 35 588 singletons) were obtained. The total length was 83 003 836 bp. 42 914 Unigenes(66.05% of the total Unigenes) were functionally annotated after all Unigenes aligned with seven functional databases(NR, NT, GO, COG, KEGG, Swissprot, Interpro). GO annotation showed that 89 644 transcripts were divided into 3 groups, which contained Biological Process(38 432 transcripts, 42.87%), Cellular Component(32 749 transcripts, 36.53%) and Molecular Function(18 463 transcripts, 20.6%). 31 580 Unigenes were annotated in KEGG database, which were divided into six groups Cellular Process, Environmental Information Processing, Genetic Information Processing, Human Disease, Metabolism, Organismal System. 18 580 Unigenes were involved in metablism at most, accounting for 58.83% of the total Unigenes annotated in KEGG database. 37 762 Unigenes were annotated in COG database, which were divided into 25 groups. The group of general function prediction only(16.9%) was the biggest, the second one was transcription(8.8%), the latter ones were replication, recombination and repair(7.8%). With the help of high-through sequencing, In this study, the possible functional genes involved in wood formation were analyzed, which might provide molecular data for exploring the molecular mechanism of wood development and further discovery of important functional genes.
Cryptomeria fortunei is an important coniferous timber tree in southern China, which has the characteristics of tall shape and straight texture. It has been widely used in plate and building material production. The characteristics of the transcriptome of vascular cambium and xylem zone were studied and analyzed, which would lay a theoretical basis for further study of the molecular mechanism and genetic regulation during the process of wood formation, and the cultivation of fine woods. In this study, cambium tissue of C. fortunei was used as test materials,and the transcriptome sequencing of C. fortunei vascular cambium at four different development stages was conducted based on Illumina Hiseq sequencing platform. The protein functional annotation, GO classification and KEGG metabolic pathway analysis of Unigene were performed. The sequencing data were analyzed according to the procedure of no-reference transcriptome sequencing. A total of 105.9 Gb data were obtained and the filtered clean reads reached more than 90%. Clean reads were assembled by Trinity software and a total of 64 969 Unigenes(29 381 contigs and 35 588 35 588 singletons) were obtained. The total length was 83 003 836 bp. 42 914 Unigenes(66.05% of the total Unigenes) were functionally annotated after all Unigenes aligned with seven functional databases(NR, NT, GO, COG, KEGG, Swissprot, Interpro). GO annotation showed that 89 644 transcripts were divided into 3 groups, which contained Biological Process(38 432 transcripts, 42.87%), Cellular Component(32 749 transcripts, 36.53%) and Molecular Function(18 463 transcripts, 20.6%). 31 580 Unigenes were annotated in KEGG database, which were divided into six groups Cellular Process, Environmental Information Processing, Genetic Information Processing, Human Disease, Metabolism, Organismal System. 18 580 Unigenes were involved in metablism at most, accounting for 58.83% of the total Unigenes annotated in KEGG database. 37 762 Unigenes were annotated in COG database, which were divided into 25 groups. The group of general function prediction only(16.9%) was the biggest, the second one was transcription(8.8%), the latter ones were replication, recombination and repair(7.8%). With the help of high-through sequencing, In this study, the possible functional genes involved in wood formation were analyzed, which might provide molecular data for exploring the molecular mechanism of wood development and further discovery of important functional genes.
引文
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Niu S.H.,Yuan H.W.,Sun X.R.,Porth I.,Li Y.,El-Kassaby Y.A.and Li W.,2016,A transcriptomics investigation into pine reproductive organ development,New Phytologist,209(3)1278-1289
Quevillon E.,Silventoinen V.,Pillai S.,Harte N.,Mulder N.,Ap weiler R.,and Lopez R.,2005,InterProScan:protein do mains identifier,Nucleic Acids Res.,33(2):116-120
Sun Y.,Li X.,Li Y.,Ye D.Q.,Shi J.S.,and Bian L.M.,2019Analysis of growth traits and morphological characters a mong different clones of Cunninghamia lanceolata in young tree stage,Zhongnan Linye Keji Daxue Xuebao(Journal o Central South University of Forestry&Technology),39(3)34-39(孙云,李鑫,李勇,叶代全,施季森,边黎明,2019幼树阶段杉木不同无性系生长与形态性状分析,中南林业科技大学学报,39(3):34-39)
Yang J.,Park S.,Kamdem D.P.,Keathley D.E.,Retzel E.,Paul C.,Kapur V.,and Han K.H.,2003,Novel gene expression profiles define the metabolic and physiological processe characteristic of wood and its extractive formation in a hard wood tree species,Robinia pseudoacacia,Plant Mol.Biol.52(5):935-956
Ambawat S.,Sharma P.,Yadav N.R.,and Yadav R.C.,2013,MYBtranscription factor genes as regulators for plant responses an overview,Physiol.Mol.Biol.Plants,19(3):307-321
Cock P.,Fields C.,Goto N.,Heuer M.,and Rice P.,2010,The Sanger FASTQ file format for sequences with quality scores,and the Solexa/Illumina FASTQ variants,Nucleic Acids Res.,38(6):1767-1771
Conesa A.,Gotz S.,Garcíagómez J.M.,Terol J.,Talón M.,and Robles M.,2005,Blast2GO:a universal tool for annotation visualization and analysis in functional genomics research Bioinformatics,21(18):3674-3676
Jewett M.C.,Oliveira A.P.,Patil K.R.,and Nielsen J.,2005,The role of high-throughput transcriptome analysis in metabolic engineering,Biotechnol.Bioprocess Eng.,10(5):385-399
Mishima K.,Fujiwara T.,Iki T.,Kuroda K.,Yamashita K.Tamura M.,Fujisawa Y.,and WatanabeEmail A.,2014Transcriptome sequencing and profiling of expressed gene in cambial zone and differentiating xylem of Japanese ceda(Cryptomeria japonica),BMC Genomics,15(1):219-250
Niu S.H.,Yuan H.W.,Sun X.R.,Porth I.,Li Y.,El-Kassaby Y.A.and Li W.,2016,A transcriptomics investigation into pine reproductive organ development,New Phytologist,209(3)1278-1289
Quevillon E.,Silventoinen V.,Pillai S.,Harte N.,Mulder N.,Ap weiler R.,and Lopez R.,2005,InterProScan:protein do mains identifier,Nucleic Acids Res.,33(2):116-120
Sun Y.,Li X.,Li Y.,Ye D.Q.,Shi J.S.,and Bian L.M.,2019Analysis of growth traits and morphological characters a mong different clones of Cunninghamia lanceolata in young tree stage,Zhongnan Linye Keji Daxue Xuebao(Journal o Central South University of Forestry&Technology),39(3)34-39(孙云,李鑫,李勇,叶代全,施季森,边黎明,2019幼树阶段杉木不同无性系生长与形态性状分析,中南林业科技大学学报,39(3):34-39)
Yang J.,Park S.,Kamdem D.P.,Keathley D.E.,Retzel E.,Paul C.,Kapur V.,and Han K.H.,2003,Novel gene expression profiles define the metabolic and physiological processe characteristic of wood and its extractive formation in a hard wood tree species,Robinia pseudoacacia,Plant Mol.Biol.52(5):935-956