De novo Sequencing and Characterization of Juvenile Sporophyte Transcriptome of a Fern, Dicranopteris dichotoma

LIU Li-ting; WEN Qiang; HUANG Xiao-chun; LIU Qi-jing

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De novo Sequencing and Characterization of Juvenile Sporophyte Transcriptome of a Fern, Dicranopteris dichotoma

1.
Beijing Forestry University, Beijing 100083, China
2.
Jiangxi Provincial Biotech Key Lab for Plant, Jiangxi Academy of Forestry, Nanchang 330032, Jiangxi, China

Received Date: 2015-11-25

Abstract

[Objective] The sporophyte transcriptome of Dicranopteris dichotoma was sequenced by Illumina MiSeq 250 to provide molecular information of its growth, development, metabolism, and the micro evolutionary mechanism. [Method] The functional annotations, metabolic pathways and microsatellite analysis of some Unigenes were conducted using bioinformatics methods. [Result] A total of 18 463 296 reads containing 4.62 Gbp of sequence information were generated. A total of 63 169 unigenes were formed by initial sequence splicing, with an average read length of 863 bp and N50 value of 1 587 bp. 26 826 unigenes were annotated using BLASTX searches against the Nr, Nt and SwissProt databases. The unigenes of the transcriptome of D. dichotoma were roughly divided into cellular components, molecule function and biological processes categories of 47 branches by gene ontology, of which related with cellular process cell, binding, metabolism processes and catalytic activities. Further annotated based on COG category, Unigenes could be grouped into 26 functional categories. KEGG pathway analysis showed that Unigenes could be divided into 276 classes based on their metabolic function. Meanwhile, 13 286 SSRs (simple sequence repeats) were mined with repeat motif of 2 to 6 bp by MISA. The trinucleotide repeats were most dominant, accounting for a total of 40.41%. AG/CT (14.45%) and AAG/CTT (12.39%) were the most common repeat motifs. Polymorphic SSR markers were developed from repeat motifs, which could be used for genotyping of different individuals of D. dichotoma. [Conclusion] A higher quality of transcriptome database was obtained in this study, which could reveal the general characteristics of gene expression in the process of growth and development, and lay the foundation for further gene function mining and the large-scale development of molecular markers of D. dichotoma.
- Dicranopteris dichotoma,
- transcriptome,
- gene annotation,
- simple sequence repeat

References

[1]	Xu X L, Li Q K, Wang J Y, et al. Inorganic and Organic Nitrogen Acquisition by a Fern Dicranopteris dichotoma in a Subtropical Forest in South China[J]. PLOS ONE, 2014, 9(5): e9005.
[2]	董鸣.克隆植物生态学[M]. 北京:科学出版社. 2011,5-6.
[3]	岩槻邦男. 日本野生植物-蕨类(日文) [M]. 东京: 平凡社. 1999,311.
[4]	张明如, 何明, 温国胜, 等. 芒萁种群特征及其对森林更新影响评述[J]. 内蒙古农业大学学报, 2010, 31(4): 303-308.
[5]	李小飞, 陈志彪, 陈志强, 等.南方红壤侵蚀区芒萁生长特征及其对环境因子的响应[J]. 水土保持通报, 2013, 33(3): 33-37.
[6]	刘迎春, 刘琪璟, 汪宏清, 等.芒萁生物量分布特征[J].生态学杂志, 2008, 27(5): 705-711.
[7]	侯晓龙, 刘明新, 蔡丽平, 等.安溪崩岗侵蚀区不同植被配置模式与恢复效果研究[J]. 亚热带水土保持, 2010, 22(1): 5-10.
[8]	Wei C Y, Wang C, Sun X, et al. Arsenic accumulation by ferns:a field survey in southern China[J]. Environmental Geochemistry and Health, 2007, 29(3):169-177.
[9]	刘足根, 杨国华, 杨帆, 等. 赣南钨矿区土壤重金属含量与植物富集特征[J].生态学杂志, 2008, 27(8): 1345-1350.
[10]	李小飞, 陈志彪, 陈志强.南方稀土采矿恢复地土壤稀土元素含量及植物吸收特征[J]. 生态学杂志, 2013, 32( 8): 2126-2132.
[11]	王立丰, 季红兵, 田维敏.重稀土矿区芒萁稀土元素精细地位及光抑制对其光合活性的影响[J]. 中国稀土学报, 2010, 28(3): 379-386.
[12]	骆永明. 金属污染土壤的植物修复[J]. 土壤, 1999, 33(5): 261-265.
[13]	李交昆, 龚育龙, 唐璐璐, 等. 金属型植物的研究进展[J]. 生命科学研究, 2011, 15(6):560-564.
[14]	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.
[15]	Wang Z W, Jiang C, Wen Q, et al. Deep sequencing of the Camellia chekiangoleosa transcriptome revealed candidate genes for anthocyanin biosynthesis[J]. Gene, 2014, 538(1):1-7.
[16]	Barker M S, Wolf P G. Unfurling fern biology in the genomics age[J]. Bioscience, 2010, 60: 177-185.
[17]	Barker M S. Evolutionary genomic analyses of ferns reveal that high chromosome numbers are a product of high retention and fewer rounds of polyploidy relative to angiosperms[J]. Amer Fern J, 2009, 99: 136-137.
[18]	Nakazato T, Barker M S, Rieseberg L H, et al. Evolution of the nuclear genome of ferns and lycophytes [M]// Ranker T A, Haufler C H.Biology and Evolution of Ferns and Lycophytes. Cambridge University Press. 2008, 175-198.
[19]	Aya K, Kobayashi M, Tanaka J, et al. De novo transcriptome assembly of a fern, Lygodium japonicum, and a web resource database, Ljtrans DB[J]. Plant & Cell Physiology, 2015, 56(1):e5.
[20]	Weng J K, Tanurdzic M, Chapple C. Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii[J]. BMC Genomics, 2005, 6: 85-97.
[21]	Yamauchi D, Sutoh K, Kanegae H, et al. Analysis of expressed sequence tags in prothallia of Adiantum capillus-veneris[J]. Journal of Plant Research, 2005, 118:223-227.
[22]	Der J D, Barker M S, Wickett N J, et al. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum[J]. BMC Genomics, 2011, 12(1):99-113.
[23]	Bushart T J, Cannon A E, Haque U L A, et al. RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): evidence for modulation by calcium pumps and apyrase activity[J]. Amer J Bot, 2013, 100: 161-174.
[24]	贾新平, 孙晓波, 邓衍明, 等. 鸟巢蕨转录组高通量测序及分析[J]. 园艺学报, 2014, 41(11): 2329-2341.
[25]	温强, 叶金山, 雷小林, 等. 油茶ISSR反应体系建立及优化[J]. 中南林学院学报, 2006, 26(6): 22-26.
[26]	Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology, 2011, 29, 644-652.
[27]	Weber J L. Infomativeness of human (dC-dA)n-(dG-dT)n polymorphisms[J]. Genomics, 1990, 7: 524-530.
[28]	Trapnell C, Williams B A, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nature Biotechnology, 2010, 28, 511-515.
[29]	全先庆, 张洪涛, 单雷, 等. 植物金属硫蛋白及其重金属解毒机制研究进展[J]. 遗传, 2006, 28(3): 375-382.
[30]	刘洪亮, 郑丽明, 刘青青, 等. 非模式生物转录组研究[J]. 遗传, 2013, 35(8): 955-970.
[31]	梁烨, 陈双燕, 刘公社. 新一代测序技术在植物转录组研究中的应用[J]. 遗传, 2011, 33(12): 1317-1326.
[32]	雷淑云, 张发起, Khan G, 等. 利用高通量测序分析青藏高原地区青杨的SSR和SNP特征[J]. 林业科学研究, 2015, 28(1): 37-43.
[33]	温强, 徐林初, 江香梅, 等. 基于454测序的油茶DNA序列微卫星观测与分析[J]. 林业科学, 2013, 49(8): 43-50.

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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De novo Sequencing and Characterization of Juvenile Sporophyte Transcriptome of a Fern, Dicranopteris dichotoma

1. Beijing Forestry University, Beijing 100083, China

2. Jiangxi Provincial Biotech Key Lab for Plant, Jiangxi Academy of Forestry, Nanchang 330032, Jiangxi, China

Received Date: 2015-11-25

Abstract: [Objective] The sporophyte transcriptome of Dicranopteris dichotoma was sequenced by Illumina MiSeq 250 to provide molecular information of its growth, development, metabolism, and the micro evolutionary mechanism. [Method] The functional annotations, metabolic pathways and microsatellite analysis of some Unigenes were conducted using bioinformatics methods. [Result] A total of 18 463 296 reads containing 4.62 Gbp of sequence information were generated. A total of 63 169 unigenes were formed by initial sequence splicing, with an average read length of 863 bp and N50 value of 1 587 bp. 26 826 unigenes were annotated using BLASTX searches against the Nr, Nt and SwissProt databases. The unigenes of the transcriptome of D. dichotoma were roughly divided into cellular components, molecule function and biological processes categories of 47 branches by gene ontology, of which related with cellular process cell, binding, metabolism processes and catalytic activities. Further annotated based on COG category, Unigenes could be grouped into 26 functional categories. KEGG pathway analysis showed that Unigenes could be divided into 276 classes based on their metabolic function. Meanwhile, 13 286 SSRs (simple sequence repeats) were mined with repeat motif of 2 to 6 bp by MISA. The trinucleotide repeats were most dominant, accounting for a total of 40.41%. AG/CT (14.45%) and AAG/CTT (12.39%) were the most common repeat motifs. Polymorphic SSR markers were developed from repeat motifs, which could be used for genotyping of different individuals of D. dichotoma. [Conclusion] A higher quality of transcriptome database was obtained in this study, which could reveal the general characteristics of gene expression in the process of growth and development, and lay the foundation for further gene function mining and the large-scale development of molecular markers of D. dichotoma.

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Reference (33)

[1]	Xu X L, Li Q K, Wang J Y, et al. Inorganic and Organic Nitrogen Acquisition by a Fern Dicranopteris dichotoma in a Subtropical Forest in South China[J]. PLOS ONE, 2014, 9(5): e9005.
[2]	董鸣.克隆植物生态学[M]. 北京:科学出版社. 2011,5-6.
[3]	岩槻邦男. 日本野生植物-蕨类(日文) [M]. 东京: 平凡社. 1999,311.
[4]	张明如, 何明, 温国胜, 等. 芒萁种群特征及其对森林更新影响评述[J]. 内蒙古农业大学学报, 2010, 31(4): 303-308.
[5]	李小飞, 陈志彪, 陈志强, 等.南方红壤侵蚀区芒萁生长特征及其对环境因子的响应[J]. 水土保持通报, 2013, 33(3): 33-37.
[6]	刘迎春, 刘琪璟, 汪宏清, 等.芒萁生物量分布特征[J].生态学杂志, 2008, 27(5): 705-711.
[7]	侯晓龙, 刘明新, 蔡丽平, 等.安溪崩岗侵蚀区不同植被配置模式与恢复效果研究[J]. 亚热带水土保持, 2010, 22(1): 5-10.
[8]	Wei C Y, Wang C, Sun X, et al. Arsenic accumulation by ferns:a field survey in southern China[J]. Environmental Geochemistry and Health, 2007, 29(3):169-177.
[9]	刘足根, 杨国华, 杨帆, 等. 赣南钨矿区土壤重金属含量与植物富集特征[J].生态学杂志, 2008, 27(8): 1345-1350.
[10]	李小飞, 陈志彪, 陈志强.南方稀土采矿恢复地土壤稀土元素含量及植物吸收特征[J]. 生态学杂志, 2013, 32( 8): 2126-2132.
[11]	王立丰, 季红兵, 田维敏.重稀土矿区芒萁稀土元素精细地位及光抑制对其光合活性的影响[J]. 中国稀土学报, 2010, 28(3): 379-386.
[12]	骆永明. 金属污染土壤的植物修复[J]. 土壤, 1999, 33(5): 261-265.
[13]	李交昆, 龚育龙, 唐璐璐, 等. 金属型植物的研究进展[J]. 生命科学研究, 2011, 15(6):560-564.
[14]	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.
[15]	Wang Z W, Jiang C, Wen Q, et al. Deep sequencing of the Camellia chekiangoleosa transcriptome revealed candidate genes for anthocyanin biosynthesis[J]. Gene, 2014, 538(1):1-7.
[16]	Barker M S, Wolf P G. Unfurling fern biology in the genomics age[J]. Bioscience, 2010, 60: 177-185.
[17]	Barker M S. Evolutionary genomic analyses of ferns reveal that high chromosome numbers are a product of high retention and fewer rounds of polyploidy relative to angiosperms[J]. Amer Fern J, 2009, 99: 136-137.
[18]	Nakazato T, Barker M S, Rieseberg L H, et al. Evolution of the nuclear genome of ferns and lycophytes [M]// Ranker T A, Haufler C H.Biology and Evolution of Ferns and Lycophytes. Cambridge University Press. 2008, 175-198.
[19]	Aya K, Kobayashi M, Tanaka J, et al. De novo transcriptome assembly of a fern, Lygodium japonicum, and a web resource database, Ljtrans DB[J]. Plant & Cell Physiology, 2015, 56(1):e5.
[20]	Weng J K, Tanurdzic M, Chapple C. Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii[J]. BMC Genomics, 2005, 6: 85-97.
[21]	Yamauchi D, Sutoh K, Kanegae H, et al. Analysis of expressed sequence tags in prothallia of Adiantum capillus-veneris[J]. Journal of Plant Research, 2005, 118:223-227.
[22]	Der J D, Barker M S, Wickett N J, et al. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum[J]. BMC Genomics, 2011, 12(1):99-113.
[23]	Bushart T J, Cannon A E, Haque U L A, et al. RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): evidence for modulation by calcium pumps and apyrase activity[J]. Amer J Bot, 2013, 100: 161-174.
[24]	贾新平, 孙晓波, 邓衍明, 等. 鸟巢蕨转录组高通量测序及分析[J]. 园艺学报, 2014, 41(11): 2329-2341.
[25]	温强, 叶金山, 雷小林, 等. 油茶ISSR反应体系建立及优化[J]. 中南林学院学报, 2006, 26(6): 22-26.
[26]	Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology, 2011, 29, 644-652.
[27]	Weber J L. Infomativeness of human (dC-dA)n-(dG-dT)n polymorphisms[J]. Genomics, 1990, 7: 524-530.
[28]	Trapnell C, Williams B A, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nature Biotechnology, 2010, 28, 511-515.
[29]	全先庆, 张洪涛, 单雷, 等. 植物金属硫蛋白及其重金属解毒机制研究进展[J]. 遗传, 2006, 28(3): 375-382.
[30]	刘洪亮, 郑丽明, 刘青青, 等. 非模式生物转录组研究[J]. 遗传, 2013, 35(8): 955-970.
[31]	梁烨, 陈双燕, 刘公社. 新一代测序技术在植物转录组研究中的应用[J]. 遗传, 2011, 33(12): 1317-1326.
[32]	雷淑云, 张发起, Khan G, 等. 利用高通量测序分析青藏高原地区青杨的SSR和SNP特征[J]. 林业科学研究, 2015, 28(1): 37-43.
[33]	温强, 徐林初, 江香梅, 等. 基于454测序的油茶DNA序列微卫星观测与分析[J]. 林业科学, 2013, 49(8): 43-50.

De novo Sequencing and Characterization of Juvenile Sporophyte Transcriptome of a Fern, Dicranopteris dichotoma

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通讯作者: 陈斌, bchen63@163.com

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De novo Sequencing and Characterization of Juvenile Sporophyte Transcriptome of a Fern, Dicranopteris dichotoma

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