生物多样性 ›› 2017, Vol. 25 ›› Issue (6): 675-682. DOI: 10.17520/biods.2017042 cstr: 32101.14.biods.2017042
所属专题: 物种形成与系统进化
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,*()
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:
Jiangping Shu1,2, Li Liu1,2, Hui Shen2, Xiling Dai1, Quanxi Wang1,4, Yuehong Yan2,3,4,*()
Received:
2017-02-18
Accepted:
2017-06-20
Online:
2017-06-20
Published:
2017-07-10
Contact:
Yan Yuehong
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。
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.
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 |
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.
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