生物多样性 ›› 2016, Vol. 24 ›› Issue (12): 1325-1334. DOI: 10.17520/biods.2016231
刘莉1,3, 舒江平1,3, 韦宏金1, 张锐1, 沈慧1,*(), 严岳鸿1,2
收稿日期:
2016-08-23
接受日期:
2016-11-09
出版日期:
2016-12-20
发布日期:
2017-01-10
通讯作者:
沈慧
作者简介:
* 通讯作者 E-mail: shenhui@sibs.ac.cn
基金资助:
Li Liu1,3, Jiangping Shu1,3, Hongjin Wei1, Rui Zhang1, Hui Shen1,*(), Yuehong Yan1,2
Received:
2016-08-23
Accepted:
2016-11-09
Online:
2016-12-20
Published:
2017-01-10
Contact:
Hui Shen
摘要:
岩穴蕨(Monachosorum maximowiczii)隶属于碗蕨科稀子蕨属, 是东亚中高海拔地区所特有的珍稀濒危植物。为了在分子水平对该物种有进一步的认识, 本文首次利用二代高通量测序技术(RNA-seq)对岩穴蕨进行了转录组测序分析。通过Illumina Hiseq 2500测序平台, 共计获得4.95 Gb原始数据(raw data), 经过滤后得到4.83 Gb有效数据(clean reads), 并进行从头组装得到了101,448条unigene。其中, 54,106条unigene预测到完整的开放阅读框。我们利用目前已知的51个植物基因组数据, 对岩穴蕨的unigene进行了详尽的功能注释, 并通过GO、COG、KEGG注释进一步了解了这些编码基因的作用方式、特征以及所参与的代谢通路。同时, 转录因子分析结果也为岩穴蕨的环境适应机制研究提供了初步线索。
刘莉, 舒江平, 韦宏金, 张锐, 沈慧, 严岳鸿 (2016) 东亚特有珍稀蕨类植物岩穴蕨(碗蕨科)高通量转录组测序及分析. 生物多样性, 24, 1325-1334. DOI: 10.17520/biods.2016231.
Li Liu, Jiangping Shu, Hongjin Wei, Rui Zhang, Hui Shen, Yuehong Yan (2016) De novo transcriptome analysis of the rare fern Monachosorum maximowiczii (Dennstaedtiaceae) endemic to East Asia. Biodiversity Science, 24, 1325-1334. DOI: 10.17520/biods.2016231.
物种名 Species | 测序部位 Description | 测序平台 Platform | 数据总量 Total size (Mb) | 单基因簇或转录本数目 No. of unigene or transcript | 文献 References |
---|---|---|---|---|---|
欧洲蕨 Pteridium aquilinum | 配子体 Gametophyte | Roche 454 | 254 | 56,256 | |
水蕨 Ceratopteris richardii | 孢子 Spore | Roche 454 | 266 | 15,730 | |
鸟巢蕨 Asplenium nidus | 叶片 Leaf | Illumina HiSeq 2000 | 5,910 | 42,907 | |
海金沙 Lygodium japonicum | 原叶体、营养叶、孢子体、根状茎 Pro- thalli, trophophylls, sporophylls, rhizomes | Roche 454 Illumina HiSeq 2000 | 28 268 | 18,999 381,814 | |
巨木贼 Equisetum giganteum | 茎、叶、孢子囊 Stem, leaf, strobili | Illumina RNA-Seq | 8,800 | 34,282 |
表1 已发表的5个蕨类植物转录组测序及组装信息
Table 1 Sequencing and assembly information of five published ferns transcriptomes
物种名 Species | 测序部位 Description | 测序平台 Platform | 数据总量 Total size (Mb) | 单基因簇或转录本数目 No. of unigene or transcript | 文献 References |
---|---|---|---|---|---|
欧洲蕨 Pteridium aquilinum | 配子体 Gametophyte | Roche 454 | 254 | 56,256 | |
水蕨 Ceratopteris richardii | 孢子 Spore | Roche 454 | 266 | 15,730 | |
鸟巢蕨 Asplenium nidus | 叶片 Leaf | Illumina HiSeq 2000 | 5,910 | 42,907 | |
海金沙 Lygodium japonicum | 原叶体、营养叶、孢子体、根状茎 Pro- thalli, trophophylls, sporophylls, rhizomes | Roche 454 Illumina HiSeq 2000 | 28 268 | 18,999 381,814 | |
巨木贼 Equisetum giganteum | 茎、叶、孢子囊 Stem, leaf, strobili | Illumina RNA-Seq | 8,800 | 34,282 |
原始数据 Raw data | 有效数据 Clean data | |
---|---|---|
序列数目 Number of sequences | 49,027,722 | 48,497,004 |
全长 Total length (Gb) | 4.95 | 4.83 |
Q20值 Q20% | 96.54% | 98.61% |
Q30值 Q30% | 91.54% | 93.58% |
GC值 GC% | 47.82% | 47.71% |
表2 岩穴蕨转录组测序及质控结果统计
Table 2 The results and qualities of sequencing for Monachosorum maximowiczii transcriptome
原始数据 Raw data | 有效数据 Clean data | |
---|---|---|
序列数目 Number of sequences | 49,027,722 | 48,497,004 |
全长 Total length (Gb) | 4.95 | 4.83 |
Q20值 Q20% | 96.54% | 98.61% |
Q30值 Q30% | 91.54% | 93.58% |
GC值 GC% | 47.82% | 47.71% |
转录本 Transcript | 单基因簇 Unigene | |
---|---|---|
序列数目 Sequence number | 107,197 | 101,448 |
平均长度 Mean length (bp) | 955 | 900 |
最大长度 Max. length (bp) | 14,804 | 14,804 |
最小长度 Min. length (bp) | 201 | 201 |
N50值 N50 | 1,907 | 1,817 |
GC含量 GC content | 0.44 | 0.44 |
表3 岩穴蕨转录组de novo组装结果统计
Table 3 Summary of de novo assembly analysis for Monachosorum maximowiczii transcriptome
转录本 Transcript | 单基因簇 Unigene | |
---|---|---|
序列数目 Sequence number | 107,197 | 101,448 |
平均长度 Mean length (bp) | 955 | 900 |
最大长度 Max. length (bp) | 14,804 | 14,804 |
最小长度 Min. length (bp) | 201 | 201 |
N50值 N50 | 1,907 | 1,817 |
GC含量 GC content | 0.44 | 0.44 |
三大类 Three categories | GO条目 GO term | Unigene 数目 No. of unigene |
---|---|---|
生物学过程 Biological process | 生物过程调控 Regulation of biological process | 1,368 |
细胞组织部分或生物合成 Cellular component organization or biogenesis | 561 | |
定位活性 Establishment of localization | 1,559 | |
免疫系统进程 Immune system process | 9 | |
单一的生物过程 Single-organism process | 5,268 | |
定位 Localization | 1,576 | |
细胞活动 Locomotion | 8 | |
生物粘附 Biological adhesion | 2 | |
刺激反应 Response to stimulus | 994 | |
细胞杀伤 Cell killing | 1 | |
繁殖进程 Reproductive process | 24 | |
生物调节 Biological regulation | 1,448 | |
代谢进程 Metabolic process | 9,458 | |
信号传导 Signaling | 393 | |
生长 Growth | 16 | |
细胞进程 Cellular process | 8,525 | |
发育进程 Developmental process | 37 | |
有机体进程 Multi-organism process | 32 | |
繁殖 Reproduction | 12 | |
生物过程的负调控 Negative regulation of biological process | 48 | |
多细胞进程 Multicellular organismal process | 54 | |
生物过程的正调控 Positive regulation of biological process | 35 | |
细胞组分 Cellular component | 细胞器部分 Organelle part | 864 |
细胞 Cell | 2,598 | |
高分子复合物 Macromolecular complex | 1,399 | |
膜结构 Membrane | 2,329 | |
胞外区域 Extracellular region | 21 | |
膜部分 Membrane part | 1,361 | |
病毒体 Virion | 1 | |
膜关闭内腔 Membrane-enclosed lumen | 150 | |
细胞部分 Cell part | 2,598 | |
细胞器 Organelle | 1,859 | |
胞外基质部分 Extracellular region part | 1 | |
胞外基质 Extracellular matrix | 1 | |
病毒体部分 Virion part | 1 | |
分子功能 Molecular function | 结合蛋白转录活性 Protein binding transcription factor activity | 60 |
鸟嘌呤核苷酸交换因子活性 Guanyl-nucleotide exchange factor activity | 33 | |
抗氧化活性 Antioxidant activity | 114 | |
受体活性 Receptor activity | 105 | |
结构分子活性 Structural molecule activity | 294 | |
分子转导活性 Molecular transducer activity | 116 | |
酶调节活性 Enzyme regulator activity | 118 | |
营养库活性 Nutrient reservoir activity | 7 | |
金属伴侣蛋白活性 Metallochaperone activity | 4 | |
催化活性 Catalytic activity | 8,722 | |
转运活性 Transporter activity | 936 | |
结合活性 Binding | 9,666 | |
电子载体活性 Electron carrier activity | 119 | |
核苷酸结合转录因子活性 Nucleic acid binding transcription factor activity | 350 |
表4 岩穴蕨unigene的GO功能类别
Table 4 GO-slim functional categories of the assembled unigene for Monachosorum maximowiczii
三大类 Three categories | GO条目 GO term | Unigene 数目 No. of unigene |
---|---|---|
生物学过程 Biological process | 生物过程调控 Regulation of biological process | 1,368 |
细胞组织部分或生物合成 Cellular component organization or biogenesis | 561 | |
定位活性 Establishment of localization | 1,559 | |
免疫系统进程 Immune system process | 9 | |
单一的生物过程 Single-organism process | 5,268 | |
定位 Localization | 1,576 | |
细胞活动 Locomotion | 8 | |
生物粘附 Biological adhesion | 2 | |
刺激反应 Response to stimulus | 994 | |
细胞杀伤 Cell killing | 1 | |
繁殖进程 Reproductive process | 24 | |
生物调节 Biological regulation | 1,448 | |
代谢进程 Metabolic process | 9,458 | |
信号传导 Signaling | 393 | |
生长 Growth | 16 | |
细胞进程 Cellular process | 8,525 | |
发育进程 Developmental process | 37 | |
有机体进程 Multi-organism process | 32 | |
繁殖 Reproduction | 12 | |
生物过程的负调控 Negative regulation of biological process | 48 | |
多细胞进程 Multicellular organismal process | 54 | |
生物过程的正调控 Positive regulation of biological process | 35 | |
细胞组分 Cellular component | 细胞器部分 Organelle part | 864 |
细胞 Cell | 2,598 | |
高分子复合物 Macromolecular complex | 1,399 | |
膜结构 Membrane | 2,329 | |
胞外区域 Extracellular region | 21 | |
膜部分 Membrane part | 1,361 | |
病毒体 Virion | 1 | |
膜关闭内腔 Membrane-enclosed lumen | 150 | |
细胞部分 Cell part | 2,598 | |
细胞器 Organelle | 1,859 | |
胞外基质部分 Extracellular region part | 1 | |
胞外基质 Extracellular matrix | 1 | |
病毒体部分 Virion part | 1 | |
分子功能 Molecular function | 结合蛋白转录活性 Protein binding transcription factor activity | 60 |
鸟嘌呤核苷酸交换因子活性 Guanyl-nucleotide exchange factor activity | 33 | |
抗氧化活性 Antioxidant activity | 114 | |
受体活性 Receptor activity | 105 | |
结构分子活性 Structural molecule activity | 294 | |
分子转导活性 Molecular transducer activity | 116 | |
酶调节活性 Enzyme regulator activity | 118 | |
营养库活性 Nutrient reservoir activity | 7 | |
金属伴侣蛋白活性 Metallochaperone activity | 4 | |
催化活性 Catalytic activity | 8,722 | |
转运活性 Transporter activity | 936 | |
结合活性 Binding | 9,666 | |
电子载体活性 Electron carrier activity | 119 | |
核苷酸结合转录因子活性 Nucleic acid binding transcription factor activity | 350 |
COG功能分类 COG function classifications | Unigene数目 No. of unigene | 百分比 Percentage (%) |
---|---|---|
RNA加工与修饰 RNA processing and modification | 576 | 4.76 |
染色质结构和活力 Chromatin structure and dynamics | 168 | 1.39 |
能量生成与转换 Energy production and conversion | 475 | 3.92 |
细胞周期控制、细胞分裂、染色体分区 Cell cycle control, cell division, chromosome partitioning | 288 | 2.38 |
氨基酸转运与代谢 Amino acid transport and metabolism | 318 | 2.63 |
核苷酸转运与代谢 Nucleotide transport and metabolism | 181 | 1.49 |
碳水化合物转运与代谢 Carbohydrate transport and metabolism | 546 | 4.51 |
辅酶转运与代谢 Coenzyme transport and metabolism | 154 | 1.27 |
脂类转运与代谢 Lipid transport and metabolism | 424 | 3.50 |
翻译、核糖体结构和生物发生 Translation, ribosomal structure and biogenesis | 562 | 4.64 |
转录 Transcription | 669 | 5.52 |
复制、重组和修复 Replication, recombination and repair | 403 | 3.33 |
细胞壁膜生物合成 Cell wall membrane biogenesis | 66 | 0.54 |
细胞运动 Cell motility | 2 | 0.02 |
翻译后修饰、蛋白质折叠、分子伴侣 Posttranslational modification, protein turnover, chaperones | 1,209 | 9.98 |
无机离子转运与代谢 Inorganic ion transport and metabolism | 315 | 2.60 |
次生代谢物合成、转运与代谢 Secondary metabolites biosynthesis, transport and catabolism | 441 | 3.64 |
一般功能预测 General function prediction only | 1,380 | 11.39 |
未知功能 Function unknown | 932 | 7.69 |
信号转导机制 Signal transduction mechanisms | 1,933 | 15.96 |
细胞内转运、分泌和小泡运输 Intracellular trafficking, secretion, and vesicular transport | 610 | 5.04 |
防卫机制 Defense mechanisms | 114 | 0.94 |
胞外结构 Extracellular structures | 56 | 0.46 |
核结构 Nuclear structure | 32 | 0.26 |
细胞骨架 Cytoskeleton | 259 | 2.14 |
表5 岩穴蕨unigene的COG分类
Table 5 Classification of the clusters of orthologous groups (COG) for Monachosorum maximowiczii
COG功能分类 COG function classifications | Unigene数目 No. of unigene | 百分比 Percentage (%) |
---|---|---|
RNA加工与修饰 RNA processing and modification | 576 | 4.76 |
染色质结构和活力 Chromatin structure and dynamics | 168 | 1.39 |
能量生成与转换 Energy production and conversion | 475 | 3.92 |
细胞周期控制、细胞分裂、染色体分区 Cell cycle control, cell division, chromosome partitioning | 288 | 2.38 |
氨基酸转运与代谢 Amino acid transport and metabolism | 318 | 2.63 |
核苷酸转运与代谢 Nucleotide transport and metabolism | 181 | 1.49 |
碳水化合物转运与代谢 Carbohydrate transport and metabolism | 546 | 4.51 |
辅酶转运与代谢 Coenzyme transport and metabolism | 154 | 1.27 |
脂类转运与代谢 Lipid transport and metabolism | 424 | 3.50 |
翻译、核糖体结构和生物发生 Translation, ribosomal structure and biogenesis | 562 | 4.64 |
转录 Transcription | 669 | 5.52 |
复制、重组和修复 Replication, recombination and repair | 403 | 3.33 |
细胞壁膜生物合成 Cell wall membrane biogenesis | 66 | 0.54 |
细胞运动 Cell motility | 2 | 0.02 |
翻译后修饰、蛋白质折叠、分子伴侣 Posttranslational modification, protein turnover, chaperones | 1,209 | 9.98 |
无机离子转运与代谢 Inorganic ion transport and metabolism | 315 | 2.60 |
次生代谢物合成、转运与代谢 Secondary metabolites biosynthesis, transport and catabolism | 441 | 3.64 |
一般功能预测 General function prediction only | 1,380 | 11.39 |
未知功能 Function unknown | 932 | 7.69 |
信号转导机制 Signal transduction mechanisms | 1,933 | 15.96 |
细胞内转运、分泌和小泡运输 Intracellular trafficking, secretion, and vesicular transport | 610 | 5.04 |
防卫机制 Defense mechanisms | 114 | 0.94 |
胞外结构 Extracellular structures | 56 | 0.46 |
核结构 Nuclear structure | 32 | 0.26 |
细胞骨架 Cytoskeleton | 259 | 2.14 |
类别 Categories | 通路 Pathways | Unigene数目 No. of unigene | 通路数 No. of pathways |
---|---|---|---|
代谢途径 Metabolism etabolism | 碳水化合物代谢 Carbohydrate metabolism | 1,511 | 15 |
脂类物质代谢 Lipid metabolism | 813 | 14 | |
辅助因子和维生素代谢 Metabolism of cofactors and vitamins | 371 | 11 | |
能量代谢 Energy metabolism | 477 | 6 | |
核苷酸代谢 Nucleotide metabolism | 446 | 2 | |
氨基酸代谢 Amino acid metabolism | 831 | 14 | |
多酮类和萜类化合物的代谢 Metabolism of terpenoids and polyketides | 224 | 8 | |
其他次生代谢产物的生物合成 Biosynthesis of other secondary metabolites | 314 | 8 | |
其他氨基酸代谢 Metabolism of other amino acids | 270 | 5 | |
多糖生物合成与代谢 Glycan biosynthesis and metabolism | 166 | 7 | |
全球与总体图 Global and overview maps 小计 Sub-total | 4,956 10,379 (73.41%) | 6 96 (75%) | |
遗传信息加工 Genetic information processing | 折叠、分类和降解 Folding, sorting and degradation | 769 | 7 |
翻译 Translation | 876 | 5 | |
转录 Transcription | 413 | 3 | |
复制与修复 Replication and repair 小计 Sub-total | 493 2,551 (18.04%) | 6 21 (16.41%) | |
环境信息处理 Environmental information processing | 信号转导 Signal transduction 膜运输 Membrane transport 小计 Sub-total | 350 36 386 (2.73%) | 2 1 3 (2.34%) |
细胞过程 Cellular processes | 运输与代谢 Transport and catabolism 小计 Sub-total | 506 506 (3.58%) | 4 4 (3.13%) |
生物系统 Organismal systems | 环境适应性 Environmental adaptation 小计 Sub-total | 252 252 (1.78%) | 2 2 (1.56%) |
人类疾病 Human diseases | 耐药性: 抗菌 Drug resistance: Antimicrobial | 7 | 1 |
内分泌与代谢性疾病 Endocrine and metabolic diseases 小计 Sub-total | 57 64 (0.45%) | 1 2 (1.56%) |
表6 岩穴蕨unigene的KEGG注释结果及分类
Table 6 The KEGG classification and metabolism pathways for the annotated unigene for Monachosorum maximowiczii
类别 Categories | 通路 Pathways | Unigene数目 No. of unigene | 通路数 No. of pathways |
---|---|---|---|
代谢途径 Metabolism etabolism | 碳水化合物代谢 Carbohydrate metabolism | 1,511 | 15 |
脂类物质代谢 Lipid metabolism | 813 | 14 | |
辅助因子和维生素代谢 Metabolism of cofactors and vitamins | 371 | 11 | |
能量代谢 Energy metabolism | 477 | 6 | |
核苷酸代谢 Nucleotide metabolism | 446 | 2 | |
氨基酸代谢 Amino acid metabolism | 831 | 14 | |
多酮类和萜类化合物的代谢 Metabolism of terpenoids and polyketides | 224 | 8 | |
其他次生代谢产物的生物合成 Biosynthesis of other secondary metabolites | 314 | 8 | |
其他氨基酸代谢 Metabolism of other amino acids | 270 | 5 | |
多糖生物合成与代谢 Glycan biosynthesis and metabolism | 166 | 7 | |
全球与总体图 Global and overview maps 小计 Sub-total | 4,956 10,379 (73.41%) | 6 96 (75%) | |
遗传信息加工 Genetic information processing | 折叠、分类和降解 Folding, sorting and degradation | 769 | 7 |
翻译 Translation | 876 | 5 | |
转录 Transcription | 413 | 3 | |
复制与修复 Replication and repair 小计 Sub-total | 493 2,551 (18.04%) | 6 21 (16.41%) | |
环境信息处理 Environmental information processing | 信号转导 Signal transduction 膜运输 Membrane transport 小计 Sub-total | 350 36 386 (2.73%) | 2 1 3 (2.34%) |
细胞过程 Cellular processes | 运输与代谢 Transport and catabolism 小计 Sub-total | 506 506 (3.58%) | 4 4 (3.13%) |
生物系统 Organismal systems | 环境适应性 Environmental adaptation 小计 Sub-total | 252 252 (1.78%) | 2 2 (1.56%) |
人类疾病 Human diseases | 耐药性: 抗菌 Drug resistance: Antimicrobial | 7 | 1 |
内分泌与代谢性疾病 Endocrine and metabolic diseases 小计 Sub-total | 57 64 (0.45%) | 1 2 (1.56%) |
编码 ID | 代谢通路名称 Pathway | unigene数目 No. of unigene | 百分比 Percentage (%) |
---|---|---|---|
ko01100 | 代谢通路 Metabolic pathways | 2,618 | 23.03 |
ko01110 | 次生代谢产物的生物合成 Biosynthesis of secondary metabolites | 1,418 | 12.47 |
ko01200 | 碳代谢 Carbon metabolism | 406 | 3.57 |
ko01230 | 氨基酸生物合成 Biosynthesis of amino acids | 330 | 2.90 |
ko03040 | 剪接体 Spliceosome | 297 | 2.61 |
ko03010 | 核糖体 Ribosome | 292 | 2.57 |
ko00500 | 淀粉与蔗糖代谢 Starch and sucrose metabolism | 263 | 2.31 |
ko04075 | 植物激素信号转导 Plant hormone signal transduction | 255 | 2.24 |
ko00230 | 嘌呤代谢 Purine metabolism | 243 | 2.14 |
ko04141 | 内质网中的蛋白质加工 Protein processing in endoplasmic reticulum | 230 | 2.02 |
表7 KEGG分类中unigene数量最多的10个代谢通路
Table 7 Top ten metabolism pathways involving unigene in KEGG
编码 ID | 代谢通路名称 Pathway | unigene数目 No. of unigene | 百分比 Percentage (%) |
---|---|---|---|
ko01100 | 代谢通路 Metabolic pathways | 2,618 | 23.03 |
ko01110 | 次生代谢产物的生物合成 Biosynthesis of secondary metabolites | 1,418 | 12.47 |
ko01200 | 碳代谢 Carbon metabolism | 406 | 3.57 |
ko01230 | 氨基酸生物合成 Biosynthesis of amino acids | 330 | 2.90 |
ko03040 | 剪接体 Spliceosome | 297 | 2.61 |
ko03010 | 核糖体 Ribosome | 292 | 2.57 |
ko00500 | 淀粉与蔗糖代谢 Starch and sucrose metabolism | 263 | 2.31 |
ko04075 | 植物激素信号转导 Plant hormone signal transduction | 255 | 2.24 |
ko00230 | 嘌呤代谢 Purine metabolism | 243 | 2.14 |
ko04141 | 内质网中的蛋白质加工 Protein processing in endoplasmic reticulum | 230 | 2.02 |
图2 岩穴蕨unigene的转录因子预测。将54,106个预测到ORF的unigene比对到拟南芥(Arabidopsis thaliana)的转录因子数据库, 预测到1,130个转录因子。
Fig. 2 Number of Monachosorum maximowiczii unigene that were predicted as transcription factors. The 54,106 unigene which had been predicted ORF were aligned to Arabidopsis thaliana in PlantTFDB v3.0, and 1,130 unigene were predicted as transcription factors.
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