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Gu X, Li L, Li S, Shi W, Zhong X, Su Y, Wang T. Adaptive evolution and co-evolution of chloroplast genomes in Pteridaceae species occupying different habitats: overlapping residues are always highly mutated. BMC PLANT BIOLOGY 2023; 23:511. [PMID: 37880608 PMCID: PMC10598918 DOI: 10.1186/s12870-023-04523-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND The evolution of protein residues depends on the mutation rates of their encoding nucleotides, but it may also be affected by co-evolution with other residues. Chloroplasts function as environmental sensors, transforming fluctuating environmental signals into different physiological responses. We reasoned that habitat diversity may affect their rate and mode of evolution, which might be evidenced in the chloroplast genome. The Pteridaceae family of ferns occupy an unusually broad range of ecological niches, which provides an ideal system for analysis. RESULTS We conducted adaptive evolution and intra-molecular co-evolution analyses of Pteridaceae chloroplast DNAs (cpDNAs). The results indicate that the residues undergoing adaptive evolution and co-evolution were mostly independent, with only a few residues being simultaneously involved in both processes, and these overlapping residues tend to exhibit high mutations. Additionally, our data showed that Pteridaceae chloroplast genes are under purifying selection. Regardless of whether we grouped species by lineage (which corresponded with ecological niches), we determined that positively selected residues mainly target photosynthetic genes. CONCLUSIONS Our work provides evidence for the adaptive evolution of Pteridaceae cpDNAs, especially photosynthetic genes, to different habitats and sheds light on the adaptive evolution and co-evolution of proteins.
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Affiliation(s)
- Xiaolin Gu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lingling Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Sicong Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Wanxin Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaona Zhong
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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2
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Coiro M, Roberts EA, Hofmann CC, Seyfullah LJ. Cutting the long branches: Consilience as a path to unearth the evolutionary history of Gnetales. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1082639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Gnetales are one of the most fascinating groups within seed plants. Although the advent of molecular phylogenetics has generated some confidence in their phylogenetic placement of Gnetales within seed plants, their macroevolutionary history still presents many unknowns. Here, we review the reasons for such unknowns, and we focus the discussion on the presence of “long branches” both in their molecular and morphological history. The increased rate of molecular evolution and genome instability as well as the numerous unique traits (both reproductive and vegetative) in the Gnetales have been obstacles to a better understanding of their evolution. Moreover, the fossil record of the Gnetales, though relatively rich, has not yet been properly reviewed and investigated using a phylogenetic framework. Despite these apparent blocks to progress we identify new avenues to enable us to move forward. We suggest that a consilience approach, involving different disciplines such as developmental genetics, paleobotany, molecular phylogenetics, and traditional anatomy and morphology might help to “break” these long branches, leading to a deeper understanding of this mysterious group of plants.
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3
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Ping J, Hao J, Li J, Yang Y, Su Y, Wang T. Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes. Ecol Evol 2022; 12:e8499. [PMID: 35136556 PMCID: PMC8809450 DOI: 10.1002/ece3.8499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein-coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non-conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non-conifers. It is more obvious that in non-conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6- to 3.1-fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2- to 3.6-fold of non-conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein-coding genes due to gene function, plant habitat, or newly acquired IRs.
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Affiliation(s)
- Jingyao Ping
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jing Hao
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jinye Li
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yiqing Yang
- College of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen UniversityShenzhenChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Li X, Li Y, Sylvester SP, Zang M, El‐Kassaby YA, Fang Y. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol 2021; 11:13401-13414. [PMID: 34646478 PMCID: PMC8495791 DOI: 10.1002/ece3.8063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.
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Affiliation(s)
- Xuan Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yongfu Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Steven Paul Sylvester
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Mingyue Zang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yanming Fang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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Dong PB, Wang RN, Afzal N, Liu ML, Yue M, Liu JN, Tan JL, Li ZH. Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations. Genomics 2021; 113:2365-2376. [PMID: 34051325 DOI: 10.1016/j.ygeno.2021.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/18/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022]
Abstract
The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.
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Affiliation(s)
- Peng-Bin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ruo-Nan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Nawal Afzal
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jian-Ni Liu
- Early Life Institute, State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an 710069, China
| | - Jiang-Li Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
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6
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Hou C, Lian H, Cai Y, Wang Y, Liang D, He B. Comparative Analyses of Full-Length Transcriptomes Reveal Gnetum luofuense Stem Developmental Dynamics. Front Genet 2021; 12:615284. [PMID: 33841494 PMCID: PMC8027257 DOI: 10.3389/fgene.2021.615284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
Genus Gnetum, of which the majority species are pantropical liana, have broad industrial uses including for string, nets, and paper production. Although numerous studies have investigated anatomical structures during stem development, the underlying molecular mechanisms that regulate this developmental trajectory in Gnetum species remain poorly understood. A total of 12 full-length transcriptomes were generated from four stem developmental stages of an arborescent representative of this genus, Gnetum luofuense, using Oxford Nanopore Technologies. The results of this analysis reveal a total of 24,151 alternative splicing (AS) and 134,391 alternative polyadenylation events. A remarkably dynamic pattern of AS events, especially in the case of intron retentions, was found across the four developmental stages while no dynamic pattern was found among transcript numbers with varied poly(A) sites. A total of 728 long non-coding RNAs were also detected; the number of cis-regulated target genes dramatically increased while no changes were found among trans-regulated target genes. In addition, a K-means clustering analysis of all full-length transcripts revealed that primary growth is associated with carbohydrate metabolism and fungi defense, while secondary growth is closely linked with photosynthesis, nitrogen transportation, and leaf ontogenesis. The use of weighted gene co-expression network analysis as well as differentially expressed transcripts reveals that bHLH, GRF, and MYB-related transcription factors are involved in primary growth, while AP2/ERF, MYB, NAC, PLAZ, and bZIP participate in G. luofuense stem secondary growth. The results of this study provide further evidence that Nanopore sequencing technology provides a cost-effective method for generating full-length transcriptome data as well as for investigating seed plant organ development.
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Affiliation(s)
- Chen Hou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,Guangdong Academy of Forestry, Guangzhou, China
| | - Huiming Lian
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,Guangdong Academy of Forestry, Guangzhou, China
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,Guangdong Academy of Forestry, Guangzhou, China
| | - Yingli Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,Guangdong Academy of Forestry, Guangzhou, China
| | - Dongcheng Liang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,Guangdong Academy of Forestry, Guangzhou, China
| | - Boxiang He
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,Guangdong Academy of Forestry, Guangzhou, China
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7
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Di Stilio VS, Ickert-Bond SM. Ephedra as a gymnosperm evo-devo model lineage. Evol Dev 2021; 23:256-266. [PMID: 33503333 DOI: 10.1111/ede.12370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/29/2020] [Accepted: 01/02/2021] [Indexed: 11/28/2022]
Abstract
Established model systems in the flowering plants have greatly advanced our understanding of plant developmental biology, facilitating in turn its investigation across diverse land plants. The reliance on a limited number of model organisms, however, constitutes a barrier for future progress in evolutionary developmental biology (evo-devo). In particular, a more thorough understanding of seed plant character evolution and of its genetic and developmental basis has been hampered in part by a lack of gymnosperm model systems, since most are trees with decades-long generation times. Guided by the premise that future model organisms should be selected based on their character diversity, rather than simply phylogenetic "position," we highlight biological questions of potential interest that can be addressed via comparative studies in Ephedra (Gnetales). In addition to having relatively small genomes and shorter generation times in comparison to most other gymnosperms, Ephedra are amenable to investigations on the evolution of the key reproductive seed plant innovations of pollination and seed dispersal, as well as on polyploidy, and adaptation to extreme environments.
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8
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Hu Y, Xing W, Song H, Zhu H, Liu G, Hu Z. Evolutionary Analysis of Unicellular Species in Chlamydomonadales Through Chloroplast Genome Comparison With the Colonial Volvocine Algae. Front Microbiol 2019; 10:1351. [PMID: 31275275 PMCID: PMC6591512 DOI: 10.3389/fmicb.2019.01351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
This study is the first determination of six chloroplast genomes of colonial volvocine algae, Colemanosphaera charkowiensis, Volvulina compacta, Pandorina colemaniae, Pandorina morum, Colemanosphaera angeleri, and Yamagishiella unicocca. Based on 55 chloroplast protein-coding genes, we compared the nonsynonymous (dN) and synonymous (dS) substitution rates between colonial volvocine algae and the other unicellular Chlamydomonadales species. When refer to the dN, we found 27 genes were significantly different, among them, 19 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). When refer to the dS, we found 10 genes were significantly different, among them, 6 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). Then we identified 14 putative fast-evolving genes and 11 putative positively selected genes of unicellular species, we analyzed the function of positively selected sites of the overlap genes of putative fast-evolving and positively selected genes, and found some sites were close to the important functional region of the proteins. Photosynthesis is the process to transform and store solar energy by chloroplast, it plays a vital role in the survival of algae, this study is the first to use the chloroplast genomes to analysis the evolutionary relationship between colonial and unicellular species in Chlamydomonadales. We found more genes have higher substitution rates in unicellular species and proposed that the fast-evolving and positively selected two genes, psbA and psbC, may help to improve the photosynthetic efficiency of unicellular species in Chlamydomonadales.
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Affiliation(s)
- Yuxin Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Weiyue Xing
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huiyin Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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9
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Ran JH, Shen TT, Wang MM, Wang XQ. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proc Biol Sci 2019; 285:rspb.2018.1012. [PMID: 29925623 DOI: 10.1098/rspb.2018.1012] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/24/2018] [Indexed: 02/04/2023] Open
Abstract
After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution.
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Affiliation(s)
- Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Ming-Ming Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China .,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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10
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Dong WL, Wang RN, Zhang NY, Fan WB, Fang MF, Li ZH. Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution. Int J Mol Sci 2018; 19:ijms19030716. [PMID: 29498674 PMCID: PMC5877577 DOI: 10.3390/ijms19030716] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/08/2023] Open
Abstract
Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.
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Affiliation(s)
- Wan-Lin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ruo-Nan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Na-Yao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wei-Bing Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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