Biodiversity Science ›› 2017, Vol. 25 ›› Issue (6): 675-682.doi: 10.17520/biods.2017042

• Original Papers • Previous Article     Next Article

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

Jiangping Shu1, 2, Li Liu1, 2, Hui Shen2, Xiling Dai1, Quanxi Wang1, 4, Yuehong Yan2, 3, 4, *()   

  1. 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:2017-07-10
  • Yan Yuehong

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

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

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."

Fig. 2

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

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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