基于系统基因组学分析揭示早期陆生植物的复杂网状进化关系

doi:10.17520/biods.2017042

生物多样性 ›› 2017, Vol. 25 ›› Issue (6): 675-682. DOI: 10.17520/biods.2017042

所属专题：物种形成与系统进化

基于系统基因组学分析揭示早期陆生植物的复杂网状进化关系

舒江平^1,², 刘莉^1,², 沈慧², 戴锡玲¹, 王全喜^1,⁴, 严岳鸿^2,^3,^4,^*()

1 上海师范大学生命与环境科学学院, 上海 200234
2 上海辰山植物园, 中国科学院上海辰山植物科学研究中心, 上海 201602
3 国家林业局华东野生濒危资源植物保育中心, 上海 201602
4 上海市资源植物功能基因组学重点实验室, 上海 201602

收稿日期:2017-02-18 接受日期:2017-06-20 出版日期:2017-06-20 发布日期:2017-07-10
通讯作者: 严岳鸿
基金资助:
上海市绿化和市容管局2015年科学技术项目(G152420)

The complex reticulate evolutionary relationships of early terrestrial plants as revealed by phylogenomics analysis

Jiangping Shu^1,², Li Liu^1,², Hui Shen², Xiling Dai¹, Quanxi Wang^1,⁴, Yuehong Yan^2,^3,^4,^*()

1 College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234
2 Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences; Shanghai Chenshan Botanical Garden, Shanghai 201602
3 East China Wild Endangered Resources Plant Conservation Center, State Forestry Administration, Shanghai 201602
4 Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai 201602

Received:2017-02-18 Accepted:2017-06-20 Online:2017-06-20 Published:2017-07-10
Contact: Yan Yuehong

摘要/Abstract

摘要：

植物由水生走向陆生的进化过程中经历了非常复杂的演化, 期间产生的大量基因的进化路线可能互不相同, 因此仅仅使用系统发育树无法呈现真实的演化关系。系统发育网络图能够清楚地展示包括垂直演化和水平演化在内的复杂网状进化关系。本文选取莱茵衣藻(Chlamydomonas reinhardtii)和4种陆生植物, 利用系统基因组学的方法, 筛选得到1,668个一对一直系同源基因, 重新构建了陆生植物的系统发育网状进化关系。结果发现, 使用不同的分析策略所得到的系统发育树不同; 对1,668个基因单独分析, 发现存在15种不同的拓扑结构; 对5个物种筛选得到的直系同源基因进行系统发育网络分析显示, 在非常稳健的系统发育网络图中, 仅仅5个物种就存在9个不同的分离支, 暗示着非常复杂的网状进化关系; 而且藻类植物与苔藓植物和石松类植物的分离支之间差异很小, 这可能是产生系统发育树冲突的原因之一, 也暗示着早期陆生植物发生了复杂的辐射演化。

关键词: 网状进化, 基因树冲突, 系统发育基因组学, 陆生植物演化, 转录组从头测序

Abstract

Plants from aquatic to terrestrial ecosystems have undergone a very complex evolution, and their evolutionary pathways of large numbers of genes may be different from one another, so that traditional phylogenetic trees cannot show true evolutionary relationships. The phylogenetic network graph is a good solution to show the complex relationships of reticulate evolution, including vertical evolution and horizontal evolution. In this paper, we selected Chlamydomonas reinhardtii and four terrestrial plants, and screened 1,668 one-to-one orthologous genes to reconstruct the phylogenetic relationship of terrestrial plants based on phylogenomics. Results showed that phylogenetic trees were different based on different analysis strategies. The 1,668 genes were analyzed separately and 15 different topologies were found. The phylogenetic network of the orthologous genes obtained from the five species was analyzed, and the results showed that in a very robust phylogenetic network map, only five species have nine different split branches, suggesting a very complex evolutionary relationship network. Futhermore, the difference in split branches between algae and bryophytes or lycophytes is very small, which may be one of the reasons influencing the phylogenetic tree conflict, and implies that early terrestrial plants underwent a complex radiate evolution.

Key words: reticulate evolution, gene tree conflict, phylogenomics, terrestrial plant evolution, de novo transcriptome

舒江平, 刘莉, 沈慧, 戴锡玲, 王全喜, 严岳鸿 (2017) 基于系统基因组学分析揭示早期陆生植物的复杂网状进化关系. 生物多样性, 25, 675-682. DOI: 10.17520/biods.2017042.

Jiangping Shu, Li Liu, Hui Shen, Xiling Dai, Quanxi Wang, Yuehong Yan (2017) The complex reticulate evolutionary relationships of early terrestrial plants as revealed by phylogenomics analysis. Biodiversity Science, 25, 675-682. DOI: 10.17520/biods.2017042.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2017042

https://www.biodiversity-science.net/CN/Y2017/V25/I6/675

图/表 4

表1 转录组和基因组组装完整性评估结果统计

Table 1 The assessment results of assembly completeness of transcriptome and genome

物种 Species	分类 Classification	BUSCO评估结果 BUSCO results
福建观音座莲 Angiopteris fokiensis	真蕨类植物 Monilophytes	C: 66.4% [S: 43.2%, D: 23.2%], F: 5.9%, M: 27.7%, n: 1440
欧洲云杉 Picea abies	种子植物 Spermatophytes	C: 34.0% [S: 28.9%, D: 5.1%], F: 7.4%, M: 58.6%, n: 1,440
江南卷柏 Selaginella moellendorffii	石松类植物 Lycophytes	C: 63.2% [S: 10.0%, D: 53.2%], F: 4.7%, M: 32.1%, n: 1,440
小立碗藓 Physcomitrella patens	苔藓植物 Bryophytes	C: 70.1% [S: 46.0%, D: 24.1%], F: 2.6%, M: 27.3%, n: 1,440
莱茵衣藻 Chlamydomonas reintmrdtii	藻类植物 Thallophytes	C: 18.8% [S: 17.9%, D: 0.9%], F: 1.7%, M: 79.5%, n: 1,440

图1 基于串联和联合的方法分析得到的系统发育树。(A)使用串联矩阵构建的最大似然树; (B)使用联合基因树构建的物种树。

Fig. 1 The phylogenetic trees based on concatenation and coalescence methods. (A) The maximum likelihood tree based on concatenation method; (B) The species tree based on coalescence method.

图2 使用最大似然法构建的15种拓扑结构的基因树。数字表示每种拓扑结构的数量。

Fig. 2 Fifteen topological structure of gene trees based on maximum likelihood method. The numbers mean the amount of the topological structure.

图3 基于1,668个基因构建的早期陆生植物的系统发育网络。数字表示每个分离支的支持率, 除了最短分离支(箭头)之外, 其他分离支的支持率都为100%; 平行的分离支为同一种分离支。

Fig. 3 The phylogenetic network of early land plants based on 1,668 genes. The numbers mean the bootstrap support of each split branch. In addition to the shortest split branch (arrow), the bootstrap support of other split branches is 100%. The parallel split branches are the same type of split branch.

参考文献 52

[1]	Arnold CA (2013) An Introduction to Paleobotany. Read Books Ltd., New York.
[2]	Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
[3]	Bohlin K (1901) Utkast till de gröna algernas och arkegoniaternas fylogeni. Almqvist & Wiksells Boktryckeri AB, Uppsala.
[4]	Bower FO (1935) Primitive land plants. Science, 81, 537-539.
[5]	Bryant D, Moulton V (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21, 255-265.
[6]	Campbell D (1899) Lectures on the Evolution of Plants. Kessinger Publishing, London.
[7]	Church AH (1919) Thalassiophyta and the Subaerial Transmigration. Oxford University Press, Oxford.
[8]	Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
[9]	Cranston KA, Hurwitz B, Ware D, Stein L, Wing RA (2009) Species trees from highly incongruent gene trees in rice. Systematic Biology, 58, 489-500.
[10]	Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27, 1164-1165.
[11]	Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution, 24, 332-340.
[12]	Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids. Molecular Biology and Evolution, 13, 873-882.
[13]	Doolittle WF (1999) Phylogenetic classification and the universal tree. Science, 284, 2124-2128.
[14]	Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, 745-749.
[15]	Dunn CW, Howison M, Zapata F (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics, 14, 330.
[16]	Eames AJ (1936) Morphology of Vascular Plants. McGraw- Hill Book Company, New York.
[17]	Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
[18]	Fritsch F (1945) Studies in the comparative morphology of the algae. IV. Algae and archegoniate plants. Annals of Botany, 9, 1-29.
[19]	Fritsch FE (1916) The algal ancestry of the higher plants. New Phytologist, 15, 233-249.
[20]	Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150-3152.
[21]	Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644-652.
[22]	Griffiths RC, Marjoram P (1996) Ancestral inference from samples of DNA sequences with recombination. Journal of Computational Biology, 3, 479-502.
[23]	Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254-267.
[24]	Huson DH, Scornavacca C (2011) A survey of combinatorial methods for phylogenetic networks. Genome Biology and Evolution, 3, 23-35.
[25]	Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature, 389, 33-39.
[26]	Li CS (1994) Origin of land plants is an important event of life evolution. Bulletin of National Natural Science Foundation of China, (4), 8-14. (in Chinese with English abstract)
	[李承森 (1994) 生物进化的重大事件——陆地植物的起源及其研究的新进展. 中国科学基金, (4), 8-14.]
[27]	Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research, 13, 2178-2189.
[28]	Mallet J (2005) Hybridization as an invasion of the genome. Trends in Ecology & Evolution, 20, 229-237.
[29]	Mirarab S, Bayzid MS, Warnow T (2016) Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Systematic Biology, 65, 366-380.
[30]	Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T (2014) ASTRAL: genome-scale coalescent- based species tree estimation. Bioinformatics, 30, 541-548.
[31]	Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science, 346, 763-767.
[32]	Nakhleh L (2010) Evolutionary phylogenetic networks: models and issues. In: Problem Solving Handbook in Computational Biology and Bioinformatics (eds Lenwood SH, Naren R), pp. 125-158. Springer, New York.
[33]	Nakhleh L (2013) Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution, 28, 719-728.
[34]	Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature, 463, 1079-1083.
[35]	Rieseberg LH (1997) Hybrid origins of plant species. Annual Review of Ecology and Systematics, 28, 359-389.
[36]	Rubinstein CV, Gerrienne P, de la Puente G, Astini R, Steemans P (2010) Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytologist, 188, 365-369.
[37]	Salichos L, Rokas A (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 497, 327-331.
[38]	Scott DH (1900) Studies in Fossil Botany. Adam & Charles Black, London.
[39]	Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210-3212.
[40]	Sneath PH (1975) Cladistic representation of reticulate evolution. Systematic Zoology, 24, 360-368.
[41]	Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
[42]	Steemans P, Le Hérissé A, Melvin J, Miller MA, Paris F, Verniers J, Wellman CH (2009) Origin and radiation of the earliest vascular land plants. Science, 324, 353.
[43]	Sukumaran J, Holder MT (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics, 26, 1569-1571.
[44]	Syvanen M (1985) Cross-species gene transfer, implications for a new theory of evolution. Journal of Theoretical Biology, 112, 333-343.
[45]	Szöllősi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012) Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences, USA, 109, 17513-17518.
[46]	Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56, 564-577.
[47]	Tofigh A, Hallett M, Lagergren J (2011) Simultaneous identification of duplications and lateral gene transfers. IEEE/ ACM Transactions on Computational Biology and Bioinformatics (TCBB), 8, 517-535.
[48]	Wellman CH, Osterloff PL, Mohiuddin U (2003) Fragments of the earliest land plants. Nature, 425, 282-285.
[49]	Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA (2014) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, USA, 111, 4859-4868.
[50]	Woodhams MD, Lockhart PJ, Holland BR (2016) Simulating and summarizing sources of gene tree incongruence. Genome Biology and Evolution, 8, 1299-1315.
[51]	Zimmermann W (1938) Phylogenie. In: Manual of Pteridology (ed. Frans V), pp. 558-618. Springer, New York.
[52]	Zou XH, Ge S (2008) Conflicting gene trees and phylogenomics. Journal of Systematics and Evolution, 46, 795-807. (in Chinese with English abstract)
	[邹新慧, 葛颂 (2008) 基因树冲突与系统发育基因组学研究. 植物分类学报, 46, 795-807.]

基于系统基因组学分析揭示早期陆生植物的复杂网状进化关系

The complex reticulate evolutionary relationships of early terrestrial plants as revealed by phylogenomics analysis

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