1
|
Sun S, Pan Z, Fu Y, Wang S, Fu P. Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae. Ecol Evol 2024; 14:e70239. [PMID: 39224159 PMCID: PMC11368500 DOI: 10.1002/ece3.70239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/09/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.
Collapse
Affiliation(s)
- Shan‐Shan Sun
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Zhi‐Yong Pan
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Yu Fu
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Shen‐Jue Wang
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Peng‐Cheng Fu
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| |
Collapse
|
2
|
Hu XZ, Guo C, Qin SY, Li DZ, Guo ZH. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae). PLANT DIVERSITY 2024; 46:344-352. [PMID: 38798728 PMCID: PMC11119509 DOI: 10.1016/j.pld.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 05/29/2024]
Abstract
Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.
Collapse
Affiliation(s)
- Xiang-Zhou Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
3
|
Zhang TT, Yan CL, Qiao JX, Yang AS, Liu ML, Kou YX, Li ZH. Demographic dynamics and molecular evolution of the rare and endangered subsect. Gerardianae of Pinus: insights from chloroplast genomes and mitochondrial DNA markers. PLANTA 2024; 259:45. [PMID: 38281265 DOI: 10.1007/s00425-023-04316-8] [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: 12/21/2023] [Indexed: 01/30/2024]
Abstract
MAIN CONCLUSION The divergence of subsect. Gerardianae was likely triggered by the uplift of the Qinghai-Tibetan Plateau and adjacent mountains. Pinus bungeana might have probably experienced expansion since Last Interglacial period. Historical geological and climatic oscillations have profoundly affected patterns of nucleotide variability, evolutionary history, and species divergence in numerous plants of the Northern Hemisphere. However, how long-lived conifers responded to geological and climatic fluctuations in East Asia remain poorly understood. Here, based on paternally inherited chloroplast genomes and maternally inherited mitochondrial DNA markers, we investigated the population demographic history and molecular evolution of subsect. Gerardianae (only including three species, Pinus bungeana, P. gerardiana, and P. squamata) of Pinus. A low level of nucleotide diversity was found in P. bungeana (π was 0.00016 in chloroplast DNA sequences, and 0.00304 in mitochondrial DNAs). The haplotype-based phylogenetic topology and unimodal distributions of demographic analysis suggested that P. bungeana probably originated in the southern Qinling Mountains and experienced rapid population expansion since Last Interglacial period. Phylogenetic analysis revealed that P. gerardiana and P. squamata had closer genetic relationship. The species divergence of subsect. Gerardianae occurred about 27.18 million years ago (Mya) during the middle to late Oligocene, which was significantly associated with the uplift of the Qinghai-Tibetan Plateau and adjacent mountains from the Eocene to the mid-Pliocene. The molecular evolutionary analysis showed that two chloroplast genes (psaI and ycf1) were under positive selection, the genetic lineages of P. bungeana exhibited higher transition and nonsynonymous mutations, which were involved with the strongly environmental adaptation. These findings shed light on the population evolutionary history of white pine species and provide striking insights for comprehension of their species divergence and molecular evolution.
Collapse
Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Chun-Li Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jin-Xia Qiao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ao-Shuang Yang
- 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
| | - Yi-Xuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, 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.
| |
Collapse
|
4
|
Xue TT, Janssens SB, Liu BB, Yu SX. Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae). Mol Phylogenet Evol 2024; 190:107956. [PMID: 37898296 DOI: 10.1016/j.ympev.2023.107956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigate phylogenetic conflict analyses within and between plastid and mitochondrial genomes using Potentilla as a case study. We generated three plastid datasets (coding, noncoding, and all-region) and one mitochondrial dataset (coding regions) to infer phylogenies based on concatenated and multispecies coalescent (MSC) methods. Conflict analyses were then performed using PhyParts and Quartet Sampling (QS). Both plastid and mitochondrial genomes divided the Potentilla into eight highly supported clades, two of which were newly identified in this study. While most organellar loci were uninformative for the majority of nodes (bootstrap value < 70%), PhyParts and QS detected conflicting signals within the two organellar genomes. Regression analyses revealed that conflict signals mainly occurred among shorter loci, whereas longer loci tended to be more concordant with the species tree. In addition, two significant disagreements between the two organellar genomes were detected, likely attributed to hybridization and/or incomplete lineage sorting. Our results demonstrate that mitochondrial genes can fully resolve the phylogenetic relationships among eight major clades of Potentilla and are not always linked with plastome in evolutionary history. Stochastic inferences appear to be the primary source of observed conflicts among the gene trees. We recommend that the loci with short sequence length or containing limited informative sites should be used cautiously in MSC analysis, and suggest the joint application of concatenated and MSC methods for phylogenetic inference using organellar genomes.
Collapse
Affiliation(s)
- Tian-Tian Xue
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium; Department of Biology, KU Leuven, Kasteelpark Arenberg 31, BE-3001 Leuven, Belgium.
| | - Bin-Bin Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Sheng-Xiang Yu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
5
|
Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae). Ecol Evol 2024; 14:e10868. [PMID: 38274863 PMCID: PMC10809029 DOI: 10.1002/ece3.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.
Collapse
Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
| |
Collapse
|
6
|
Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
Collapse
Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| |
Collapse
|
7
|
Villaverde T, Larridon I, Shah T, Fowler RM, Chau JH, Olmstead RG, Sanmartín I. Phylogenomics sheds new light on the drivers behind a long-lasting systematic riddle: the figwort family Scrophulariaceae. THE NEW PHYTOLOGIST 2023; 240:1601-1615. [PMID: 36869601 DOI: 10.1111/nph.18845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification. We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns. Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa. Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity.
Collapse
Affiliation(s)
- Tamara Villaverde
- Real Jardín Botánico (CSIC), Plaza de Murillo, 2, Madrid, 28014, Spain
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Toral Shah
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - John H Chau
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98155, USA
| | - Isabel Sanmartín
- Real Jardín Botánico (CSIC), Plaza de Murillo, 2, Madrid, 28014, Spain
| |
Collapse
|
8
|
Simmons MP, Goloboff PA, Stöver BC, Springer MS, Gatesy J. Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses. Cladistics 2023; 39:418-436. [PMID: 37096985 DOI: 10.1111/cla.12540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/22/2023] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-tree branches with 0% approximate-likelihood-ratio-test (SH-like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (congsort), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson-Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene-tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent-tree clades that contradicted concatenation-tree clades were generally less robust to gene-tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene-tree clades (0% SH-like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony-based analyses) for improving quantification of gene-tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene-tree-estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets.
Collapse
Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Pablo A Goloboff
- CONICET, INSUE, Fundación Miguel Lillo, Miguel Lillo 251, 4000, S.M. de Tucumán, Argentina
| | - Ben C Stöver
- Institute for Evolution and Biodiversity, WMU Münster, 48149, Münster, Germany
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| |
Collapse
|
9
|
Liu TJ, Zhang SY, Wei L, Lin W, Yan HF, Hao G, Ge XJ. Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae). BMC PLANT BIOLOGY 2023; 23:359. [PMID: 37452336 PMCID: PMC10347800 DOI: 10.1186/s12870-023-04363-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Lysimachia L., the second largest genus within the subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is the species diversity center of Lysimachia, containing approximately 150 species. Despite advances in the backbone phylogeny of Lysimachia, species-level relationships remain poorly understood due to limited genomic information. This study analyzed 50 complete plastomes for 46 Lysimachia species. We aimed to identify the plastome structure features and hypervariable loci of Lysimachia. Additionally, the phylogenetic relationships and phylogenetic conflict signals in Lysimachia were examined. RESULTS These fifty plastomes within Lysimachia had the typical quadripartite structure, with lengths varying from 152,691 to 155,784 bp. Plastome size was positively correlated with IR and intron length. Thirteen highly variable regions in Lysimachia plastomes were identified. Additionally, ndhB, petB and ycf2 were found to be under positive selection. Plastid ML trees and species tree strongly supported that L. maritima as sister to subg. Palladia + subg. Lysimachia (Christinae clade), while the nrDNA ML tree clearly placed L. maritima and subg. Palladia as a sister group. CONCLUSIONS The structures of these plastomes of Lysimachia were generally conserved, but potential plastid markers and signatures of positive selection were detected. These genomic data provided new insights into the interspecific relationships of Lysimachia, including the cytonuclear discordance of the position of L. maritima, which may be the result of ghost introgression in the past. Our findings have established a basis for further exploration of the taxonomy, phylogeny and evolutionary history within Lysimachia.
Collapse
Affiliation(s)
- Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Shu-Yan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, 510650, China
| |
Collapse
|
10
|
Zhao J, Zhou X, Fang S, Zhu Z, Li Y, Yu H, He Z. Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:2237. [PMID: 37375862 DOI: 10.3390/plants12122237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/07/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framework for the evolution of Marattiaceae was provided. Using both concatenation- and coalescent-based phylogenies, the gene-tree discordance, incomplete lineage sorting (ILS) simulations, and network inference were examined. Except the low support with mitochondrial genes of Marattiaceae, nuclear genes and chloroplast genes strongly supported a sister relationship between Marattiaceae and leptosporangiate ferns. At the genus level, all phylogenetic analysis based on nuclear genes datasets recovered five genera in Marattiaceae as monophyletic with strong support. Danaea and Ptisana were the first two diverged clades in turn. Christensenia was a sister clade to the clade Marattia + Angiopteris s.l. In Angiopteris s.l., three clades (Angiopteris s.s., the Archangiopteris group, and An. sparsisora) were well identified with maximum support. The Archangiopteris group was derived from Angiopteris s.s. at ca. 18 Ma. The putative hybrid species An. sparsisora between Angiopteris s.s. and the Archangiopteris group was verified by the species network analyses and the maternal plastid genes. This study will improve our understanding for using the phylotranscriptomic method to explore phylogeny and investigate hybridization events for difficult taxa in ferns.
Collapse
Affiliation(s)
- Jing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
- School of Life Sciences, Yunnan University, East Outer Ring Road, Chenggong District, Kunming 650500, China
| | - Xinmao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Shaoli Fang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Zhangming Zhu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Yuxin Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Hong Yu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Zhaorong He
- School of Life Sciences, Yunnan University, East Outer Ring Road, Chenggong District, Kunming 650500, China
| |
Collapse
|
11
|
Zhou SM, Wang F, Yan SY, Zhu ZM, Gao XF, Zhao XL. Phylogenomics and plastome evolution of Indigofera (Fabaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1186598. [PMID: 37346129 PMCID: PMC10280451 DOI: 10.3389/fpls.2023.1186598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Introduction Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera. Methods Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae. Results and discussion The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.
Collapse
Affiliation(s)
- Sheng-Mao Zhou
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Fang Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Si-Yuan Yan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Zhang-Ming Zhu
- School of Ecology and Environmental Science and Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
| | - Xin-Fen Gao
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xue-Li Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| |
Collapse
|
12
|
Tyszka AS, Bretz EC, Robertson HM, Woodcock-Girard MD, Ramanauskas K, Larson DA, Stull GW, Walker JF. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1125107. [PMID: 37063179 PMCID: PMC10098128 DOI: 10.3389/fpls.2023.1125107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.
Collapse
Affiliation(s)
- Alexa S. Tyszka
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Eric C. Bretz
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Holly M. Robertson
- Sainsbury Laboratory, School of Biological Sciences, University of Cambridge, Cambridge, England, United Kingdom
| | - Miles D. Woodcock-Girard
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Karolis Ramanauskas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Drew A. Larson
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Gregory W. Stull
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Joseph F. Walker
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| |
Collapse
|
13
|
Xie P, Tang L, Luo Y, Liu C, Yan H. Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae. BIOLOGY 2023; 12:biology12020263. [PMID: 36829541 PMCID: PMC9953724 DOI: 10.3390/biology12020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/21/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023]
Abstract
Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.
Collapse
Affiliation(s)
- Pingxuan Xie
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lilei Tang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yanzhen Luo
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Changkun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Hanjing Yan
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Key Laboratory of State Administration of Traditional Chinese Medicine for Production and Development of Cantonese Medicinal Materials, Guangzhou 510006, China
- Correspondence:
| |
Collapse
|
14
|
Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
Collapse
Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| |
Collapse
|
15
|
Yang Z, Ma W, Yang X, Wang L, Zhao T, Liang L, Wang G, Ma Q. Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales). BMC PLANT BIOLOGY 2022; 22:611. [PMID: 36566190 PMCID: PMC9789603 DOI: 10.1186/s12870-022-03991-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae. RESULTS All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi > 0.02) and five noncoding regions (Pi > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution. CONCLUSIONS Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.
Collapse
Affiliation(s)
- Zhen Yang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Goettingen, Germany
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Tiantian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Qinghua Ma
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China.
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
| |
Collapse
|
16
|
Reginato M. A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 2022; 10:e14525. [PMID: 36523475 PMCID: PMC9745922 DOI: 10.7717/peerj.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling. Methods A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented. Results A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries). Discussion Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.
Collapse
|
17
|
Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.
Collapse
Affiliation(s)
- Ting Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting-Zhang Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Si-Si Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Tuo Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jiang-Ping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yu-Nong Mu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kang-Lin Wang
- Green Development Institute, Southwest Forestry University, Kunming, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jian-Ying Xiang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| |
Collapse
|
18
|
Chen YP, Zhao F, Paton AJ, Sunojkumar P, Gao LM, Xiang CL. Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:985488. [PMID: 36160976 PMCID: PMC9493350 DOI: 10.3389/fpls.2022.985488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
As one of the largest genera of Lamiaceae and of great medicinal importance, Isodon is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within Isodon especially Clade IV using plastome sequences with a broad taxon sampling of ca. 80% species of the genus. To reduce systematic errors, twelve different plastome data sets (coding and non-coding regions with ambiguously aligned regions and saturated loci removed or not) were employed to reconstruct phylogeny using maximum likelihood and Bayesian inference. Our results revealed largely congruent topologies of the 12 data sets and recovered major lineages of Isodon consistent with previous studies, but several incongruences are also found among these data sets and among single plastid loci. Most of the shallow nodes within Clade IV were resolved with high support but extremely short branch lengths in plastid trees, and showed tremendous conflicts with the nrDNA tree, morphology and geographic distribution. These incongruences may largely result from stochasticity (due to insufficient phylogenetic signal) and hybridization and plastid capture. Therefore, the uniparental-inherited plastome sequences are insufficient to disentangle relationships within a genus which has undergone recent rapid diversification. Our findings highlight a need for additional data from nuclear genome to resolve the relationships within Clade IV and more focused studies to assess the influences of multiple processes in the evolutionary history of Isodon. Nevertheless, the morphology of the shape and surface sculpture/indumentum of nutlets is of systematic importance that they can distinguish the four major clades of Isodon.
Collapse
Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Fei Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Alan J. Paton
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
19
|
Hatami E, Jones KE, Kilian N. New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq). FRONTIERS IN PLANT SCIENCE 2022; 13:851716. [PMID: 35873957 PMCID: PMC9298463 DOI: 10.3389/fpls.2022.851716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
Collapse
Affiliation(s)
- Elham Hatami
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Katy E. Jones
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Norbert Kilian
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
20
|
Liu BB, Ren C, Kwak M, Hodel RGJ, Xu C, He J, Zhou WB, Huang CH, Ma H, Qian GZ, Hong DY, Wen J. Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1020-1043. [PMID: 35274452 DOI: 10.1111/jipb.13246] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
Collapse
Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Myounghai Kwak
- National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wen-Bin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, 27965, NC, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, 510D Mueller Laboratory, University Park, Pennsylvania, 16802, USA
| | - Guan-Ze Qian
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| |
Collapse
|
21
|
Liu J, Lindstrom AJ, Gong X. Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis. BMC PLANT BIOLOGY 2022; 22:116. [PMID: 35291941 PMCID: PMC8922756 DOI: 10.1186/s12870-022-03491-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections. RESULTS All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny. CONCLUSIONS Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.
Collapse
Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, 20250, Bangsalae, Sattahip, Chonburi, Thailand.
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
22
|
Choi IS, Cardoso D, de Queiroz LP, de Lima HC, Lee C, Ruhlman TA, Jansen RK, Wojciechowski MF. Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics. FRONTIERS IN PLANT SCIENCE 2022; 13:823190. [PMID: 35283880 PMCID: PMC8905342 DOI: 10.3389/fpls.2022.823190] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/31/2022] [Indexed: 05/31/2023]
Abstract
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
Collapse
Affiliation(s)
- In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Luciano P. de Queiroz
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | | |
Collapse
|
23
|
Sielemann K, Pucker B, Schmidt N, Viehöver P, Weisshaar B, Heitkam T, Holtgräwe D. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 2022; 23:113. [PMID: 35139817 PMCID: PMC8830136 DOI: 10.1186/s12864-022-08336-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. Results We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. Conclusion In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08336-8.
Collapse
Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
| | - Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
| |
Collapse
|
24
|
Casola C, Li J. Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C 4 plants. PeerJ 2022; 10:e12791. [PMID: 35127287 PMCID: PMC8801178 DOI: 10.7717/peerj.12791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. METHODS Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. RESULTS The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta' subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway.
Collapse
Affiliation(s)
- Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
- Interdisciplinary Graduate Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States of America
| | - Jingjia Li
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
| |
Collapse
|
25
|
Pouchon C, Boyer F, Roquet C, Denoeud F, Chave J, Coissac E, Alsos IG, Lavergne S. ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications. Mol Ecol Resour 2022; 22:2018-2037. [PMID: 35015377 DOI: 10.1111/1755-0998.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in non-model organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: 1) global sequence assembly, 2) mapping against reference sequences, and 3) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and non-coding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g. ultra-conserved elements) or collections of single-copy ortholog genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and 4 RNAseq libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 license and is available at: https://github.com/cpouchon/ORTHOSKIM.
Collapse
Affiliation(s)
- Charles Pouchon
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Cristina Roquet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057, Evry, France
| | - Jérome Chave
- Laboratoire Évolution et Diversité Biologique (EDB), UMR CNRS-IRD-UPS 5174, 31062, Toulouse Cedex, France
| | - Eric Coissac
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | | | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| |
Collapse
|
26
|
Balbinott N, Rodrigues NF, Guzman FL, Turchetto-Zolet AC, Margis R. Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies. Genet Mol Biol 2022; 45:e20210191. [PMID: 35088818 PMCID: PMC8796035 DOI: 10.1590/1678-4685-gmb-2021-0191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/20/2021] [Indexed: 05/05/2023] Open
Abstract
Myrtaceae is a large and species-rich family of woody eudicots, with prevalent
distribution in the Southern Hemisphere. Classification and taxonomy of species
belonging to this family is quite challenging, sometimes with difficulty in
species identification and producing phylogenies with low support for species
relationships. Most of the current knowledge comes from few molecular markers,
such as plastid genes and intergenic regions, which can be difficult to handle
and produce conflicting results. Based on plastid protein-coding sequences and
nuclear markers, we present a topology for the phylogenetic relationships among
Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over
previous analysis with fewer markers. Plastome phylogeny groups the tribes
Syzygieae and Eucalypteae and individual chloroplast genes produce divergent
topologies, especially among species within Myrteae tribe, but also in regard to
the grouping of Syzygieae and Eucalypteae. Results are consistent and
reproducible with both nuclear and organellar datasets. It confronts previous
data about the deep nodes of Myrtaceae phylogeny.
Collapse
Affiliation(s)
- Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| | | | - Frank Lino Guzman
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Innovación Agraria, Perú
| | | | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| |
Collapse
|
27
|
Morales-Briones DF, Gehrke B, Huang CH, Liston A, Ma H, Marx HE, Tank DC, Yang Y. Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae). Syst Biol 2021; 71:190-207. [PMID: 33978764 PMCID: PMC8677558 DOI: 10.1093/sysbio/syab032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022] Open
Abstract
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here, we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration and inferring orthologs from target enrichment data, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach, we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here, we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic data sets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.[Alchemilla; allopolyploidy; autopolyploidy; gene tree discordance; orthology inference; paralogs; Rosaceae; target enrichment; whole genome duplication.].
Collapse
Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844, USA
| | - Berit Gehrke
- University Gardens, University Museum, University of Bergen, Mildeveien 240, 5259 Hjellestad, Norway
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, 510D Mueller Laboratory, University Park, PA 16802 USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - David C Tank
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
| |
Collapse
|
28
|
Wei R, Yang J, He LJ, Liu HM, Hu JY, Liang SQ, Wei XP, Zhao CF, Zhang XC. Plastid phylogenomics provides novel insights into the infrafamilial relationship of Polypodiaceae. Cladistics 2021; 37:717-727. [PMID: 34841589 DOI: 10.1111/cla.12461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 01/01/2023] Open
Abstract
The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among closely related clades, and the phylogenetic placement of recalcitrant species or lineages. Here, we investigated the deep phylogenetic relationships within Polypodiaceae by sampling all major lineages and using 81 plastid genomes (plastomes), of which 70 plastomes were newly sequenced with high-throughput sequencing technology. Based on parsimony, maximum-likelihood, Bayesian and multispecies coalescent analyses of genome skimming data, we achieved a better resolution of the backbone phylogeny of Polypodiaceae. Using simulated data matrices, we detected that potential phylogenetic artefacts, such as long-branch attraction and insufficient taxonomic sampling, may have a confounding impact on the incongruence of phylogenetic inferences. Furthermore, our phylogenetic analyses offer greater resolution than previous multilocus studies, providing a robust framework for future phylogenetic implications on the subfamilial taxonomy of Polypodiaceae. Our phylogenomic study not only demonstrates the advantage of a character-rich plastome dataset for resolving the recalcitrant lineages that have undergone rapid radiation, but also sheds new light on integrative explorations understanding the evolutionary history of large fern groups in the genomic era.
Collapse
Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Juan He
- Xiamen Overseas Chinese Subtropical Plant Introduction Garden/Plant Introduction & Quarantine and Plant Product Key Laboratory of Xiamen, Xiamen, Fujian, 361002, China
| | - Hong-Mei Liu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Jia-Yu Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si-Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue-Ping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Cun-Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
29
|
Escobari B, Borsch T, Quedensley TS, Gruenstaeudl M. Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances. AMERICAN JOURNAL OF BOTANY 2021; 108:2235-2256. [PMID: 34636417 DOI: 10.1002/ajb2.1775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. METHODS We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. RESULTS Our results indicate that the inclusion of all plastid genome partitions is needed to infer well-supported phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. CONCLUSIONS The concatenation and combined analysis of all plastid genome partitions and the construction of manually-curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of well-supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.
Collapse
Affiliation(s)
- Belen Escobari
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, 14195, Germany
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, Casilla, La Paz, 10077, Bolivia
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, 14195, Germany
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| | - Taylor S Quedensley
- Department of Biology, Texas Christian University, Fort Worth, TX, 76109, USA
| | - Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| |
Collapse
|
30
|
Trad RJ, Cabral FN, Bittrich V, Silva SRD, Amaral MDCED. Calophyllaceae plastomes, their structure and insights in relationships within the clusioids. Sci Rep 2021; 11:20712. [PMID: 34671062 PMCID: PMC8528878 DOI: 10.1038/s41598-021-99178-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
A complete chloroplast genome is not yet available for numerous species of plants. Among the groups that lack plastome information is the clusioid clade (Malpighiales), which includes five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae, and Podostemaceae. With around 2200 species, it has few published plastomes and most of them are from Podostemaceae. Here we assembled and compared six plastomes from members of the clusioids: five from Calophyllaceae (newly sequenced) and one from Clusiaceae. Putative regions for evolutionary studies were identified and the newly assembled chloroplasts were analyzed with other available chloroplasts for the group, focusing on Calophyllaceae. Our results mostly agree with recent studies which found a general conserved structure, except for the two Podostemaceae species that have a large inversion (trnK-UUU–rbcL) and lack one intron from ycf3. Within Calophyllaceae we observed a longer LSC and reduced IRs in Mahurea exstipulata, resulting in some genic rearrangement, and a short inversion (psbJ–psbE) in Kielmeyera coriacea. Phylogenetic analyses recovered the clusioids and the five families as monophyletic and revealed that conflicts in relationships reported in the literature for the group agree with nodes concentrating uninformative or conflicting gene trees. Our study brings new insights about clusioid plastome architecture and its evolution.
Collapse
Affiliation(s)
- Rafaela Jorge Trad
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), CP 6109, Campinas, SP, 13083-970, Brazil. .,Macroecology Lab @ J3-166, Institute of Biological Sciences - ICB, Federal University of Minas Gerais (UFMG), Belo Horizonte, Campinas, MG, 31270-901, Brazil.
| | - Fernanda Nunes Cabral
- Departamento de Ciências e Linguagens, Instituto Federal de Minas Gerais - Campus Bambuí, Bambuí, MG, 38900-000, Brazil
| | - Volker Bittrich
- Volker Bittrich is an independent scientist, Campinas, Brazil
| | - Saura Rodrigues da Silva
- Department of Technology, UNESP - São Paulo State University, Campus Jaboticabal, Jaboticabal, SP, 14884-900, Brazil
| | | |
Collapse
|
31
|
Du XY, Lu JM, Zhang LB, Wen J, Kuo LY, Mynssen CM, Schneider H, Li DZ. Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic. Cladistics 2021; 37:518-539. [PMID: 34570931 DOI: 10.1111/cla.12457] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.
Collapse
Affiliation(s)
- Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming, Yunnan, 650201, China
| | - Jin-Mei Lu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Claudine M Mynssen
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, Rio de Janeiro, RJ, 22460-030, Brazil
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666000, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming, Yunnan, 650201, China
| |
Collapse
|
32
|
Stull GW, Qu XJ, Parins-Fukuchi C, Yang YY, Yang JB, Yang ZY, Hu Y, Ma H, Soltis PS, Soltis DE, Li DZ, Smith SA, Yi TS. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. NATURE PLANTS 2021; 7:1015-1025. [PMID: 34282286 DOI: 10.1038/s41477-021-00964-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/10/2021] [Indexed: 05/15/2023]
Abstract
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution-including gene and genome duplication, genome size, and chromosome number-with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.
Collapse
Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | | | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Yun Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| |
Collapse
|
33
|
Aecyo P, Marques A, Huettel B, Silva A, Esposito T, Ribeiro E, Leal IR, Gagnon E, Souza G, Pedrosa-Harand A. Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics. PLANTA 2021; 254:27. [PMID: 34236509 DOI: 10.1007/s00425-021-03655-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses. Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four ndh genes in Erythrostemon gilliesii. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from Cenostigma microphyllum for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of C. microphyllum in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.
Collapse
Affiliation(s)
- Paulo Aecyo
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana Silva
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Tiago Esposito
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Elâine Ribeiro
- Laboratory of Plant-Animal Interaction, Department of Botany, Federal University of Pernambuco, Recife, Brazil
- Laboratory of Biodiversity and Evolutionary Genetics, University of Pernambuco - Campus Petrolina, Petrolina, Brazil
| | - Inara R Leal
- Laboratory of Plant-Animal Interaction, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden of Edinburgh, University of Edinburgh, Edinburgh, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
| |
Collapse
|
34
|
Turudić A, Liber Z, Grdiša M, Jakše J, Varga F, Šatović Z. Towards the Well-Tempered Chloroplast DNA Sequences. PLANTS 2021; 10:plants10071360. [PMID: 34371563 PMCID: PMC8309291 DOI: 10.3390/plants10071360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
With the development of next-generation sequencing technology and bioinformatics tools, the process of assembling DNA sequences has become cheaper and easier, especially in the case of much shorter organelle genomes. The number of available DNA sequences of complete chloroplast genomes in public genetic databases is constantly increasing and the data are widely used in plant phylogenetic and biotechnological research. In this work, we investigated possible inconsistencies in the stored form of publicly available chloroplast genome sequence data. The impact of these inconsistencies on the results of the phylogenetic analysis was investigated and the bioinformatic solution to identify and correct inconsistencies was implemented. The whole procedure was demonstrated using five plant families (Apiaceae, Asteraceae, Campanulaceae, Lamiaceae and Rosaceae) as examples.
Collapse
Affiliation(s)
- Ante Turudić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-91-3141592
| | - Zlatko Liber
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
- Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
| | - Martina Grdiša
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| | - Jernej Jakše
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
| | - Filip Varga
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia; (M.G.); (F.V.); (Z.Š.)
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| |
Collapse
|
35
|
Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
Collapse
Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | |
Collapse
|
36
|
Doyle JJ. Defining coalescent genes: Theory meets practice in organelle phylogenomics. Syst Biol 2021; 71:476-489. [PMID: 34191012 DOI: 10.1093/sysbio/syab053] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.
Collapse
Affiliation(s)
- Jeff J Doyle
- Plant Biology Section, Plant Breeding & Genetics Section, and L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
37
|
Thode VA, Oliveira CT, Loeuille B, Siniscalchi CM, Pirani JR. Comparative analyses of Mikania (Asteraceae: Eupatorieae) plastomes and impact of data partitioning and inference methods on phylogenetic relationships. Sci Rep 2021; 11:13267. [PMID: 34168241 PMCID: PMC8225666 DOI: 10.1038/s41598-021-92727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/15/2021] [Indexed: 11/09/2022] Open
Abstract
We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole.
Collapse
Affiliation(s)
- Verônica A Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | - Caetano T Oliveira
- Sítio Roberto Burle Marx, Instituto do Patrimônio Histórico e Artístico Nacional, Estrada Roberto Burle Marx, 2019, Barra de Guaratiba, Rio de Janeiro, Rio de Janeiro, 23020-240, Brazil
| | - Benoît Loeuille
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Recife, Pernambuco, 50670-901, Brazil
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, 295 Lee Blvd, Mississippi State, Mississippi, MS, 39762, USA.
| | - José R Pirani
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Tv. 14, São Paulo, São Paulo, 05508-090, Brazil
| |
Collapse
|
38
|
Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
Collapse
Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| |
Collapse
|
39
|
Šlenker M, Kantor A, Marhold K, Schmickl R, Mandáková T, Lysak MA, Perný M, Caboňová M, Slovák M, Zozomová-Lihová J. Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides. FRONTIERS IN PLANT SCIENCE 2021; 12:659275. [PMID: 33995457 PMCID: PMC8115912 DOI: 10.3389/fpls.2021.659275] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/10/2021] [Indexed: 05/19/2023]
Abstract
Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.
Collapse
Affiliation(s)
- Marek Šlenker
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Kantor
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Karol Marhold
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin A. Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Michaela Caboňová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Judita Zozomová-Lihová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| |
Collapse
|
40
|
Bateman RM. Phenotypic versus genotypic disparity in the Eurasian orchid genus Gymnadenia: exploring the limits of phylogeny reconstruction. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1877845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richard M. Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond TW9 3DS, Surrey, UK
| |
Collapse
|
41
|
Zhang W, Wang H, Dong J, Zhang T, Xiao H. Comparative chloroplast genomes and phylogenetic analysis of Aquilegia. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11412. [PMID: 33854846 PMCID: PMC8027367 DOI: 10.1002/aps3.11412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
PREMISE Aquilegia is an ideal taxon for studying the evolution of adaptive radiation. Current phylogenies of Aquilegia based on different molecular markers are inconsistent, and therefore a clear and accurate phylogeny remains uncertain. Analyzing the chloroplast genome, with its simple structure and low recombination rate, may help solve this problem. METHODS Next-generation sequencing data were generated or downloaded for Aquilegia species, enabling their chloroplast genomes to be assembled. The assemblies were used to estimate the genome characteristics and infer the phylogeny of Aquilegia. RESULTS In this study, chloroplast genome sequences were assembled for Aquilegia species distributed across Asia, North America, and Europe. Three of the genes analyzed (petG, rpl36, and atpB) were shown to be under positive selection and may be related to adaptation. The phylogenetic tree of Aquilegia showed that its member species formed two clades with high support, North American and European species, with the Asian species being paraphyletic; A. parviflora and A. amurensis clustered with the North American species, while the remaining Asian species were found in the European clade. In addition, A. oxysepala var. kansuensis should be considered as a separate species rather than a variety. DISCUSSION The complete chloroplast genomes of these Aquilegia species provide new insights into the reconstruction of the phylogeny of related species and contribute to the further study of this genus.
Collapse
Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Jianhua Dong
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| |
Collapse
|
42
|
Daniell H, Jin S, Zhu X, Gitzendanner MA, Soltis DE, Soltis PS. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:430-447. [PMID: 33484606 PMCID: PMC7955891 DOI: 10.1111/pbi.13556] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.
Collapse
Affiliation(s)
- Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin‐Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | | | - Douglas E. Soltis
- Florida Museum of Natural History and Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| |
Collapse
|
43
|
Steenwyk JL, Buida TJ, Labella AL, Li Y, Shen XX, Rokas A. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics 2021; 37:2325-2331. [PMID: 33560364 PMCID: PMC8388027 DOI: 10.1093/bioinformatics/btab096] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes, and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock, and collapsing bipartitions (internal branches) with low support. RESULTS To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene-gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes; and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining, and deriving biological meaning from increasingly large phylogenomic datasets. AVAILABILITY PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/), and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT). SUPPLEMENTARY INFORMATION Supplementary data are available on figshare (doi: 10.6084/m9.figshare.13118600) and are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, United States of America
| | - Thomas J Buida
- 9 City Place #312, Nashville, TN, 37209, United States of America
| | - Abigail L Labella
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, United States of America
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, United States of America
| | - Xing-Xing Shen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, United States of America
| |
Collapse
|
44
|
Bateman RM, Rudall PJ, Murphy ARM, Cowan RS, Devey DS, Peréz-Escobar OA. Whole plastomes are not enough: phylogenomic and morphometric exploration at multiple demographic levels of the bee orchid clade Ophrys sect. Sphegodes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:654-681. [PMID: 33449086 DOI: 10.1093/jxb/eraa467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/15/2020] [Indexed: 05/21/2023]
Abstract
Plastid sequences have long dominated phylogeny reconstruction at all time depths, predicated on a usually untested assumption that they accurately represent the evolutionary histories of phenotypically circumscribed species. We combined detailed in situ morphometrics (124 plants) and whole-plastome sequencing through genome skimming (71 plants) in order to better understand species-level diversity and speciation in arguably the most challenging monophyletic group within the taxonomically controversial, pseudo-copulatory bee orchid genus Ophrys. Using trees and ordinations, we interpreted the data at four nested demographic levels-macrospecies, mesospecies, microspecies, and local population-seeking the optimal level for bona fide species. Neither morphological nor molecular discontinuities are evident at any level below macrospecies, the observed overlap among taxa suggesting that both mesospecies and microspecies reflect arbitrary division of a continuum of variation. Plastomes represent geographic location more strongly than taxonomic assignment and correlate poorly with morphology, suggesting widespread plastid capture and possibly post-glacial expansion from multiple southern refugia. As they are rarely directly involved in the speciation process, plastomes depend on extinction of intermediate lineages to provide phylogenetic signal and so cannot adequately document evolutionary radiations. The popular 'ethological' evolutionary model recognizes as numerous 'ecological species' (microspecies) lineages perceived as actively diverging as a result of density-dependent selection on very few features that immediately dictate extreme pollinator specificity. However, it is assumed rather than demonstrated that the many microspecies are genuinely diverging. We conversely envisage a complex four-dimensional reticulate network of lineages, generated locally and transiently through a wide spectrum of mechanisms, but each unlikely to maintain an independent evolutionary trajectory long enough to genuinely speciate by escaping ongoing gene flow. The frequent but localized microevolution that characterizes the Ophrys sphegodes complex is often convergent and rarely leads to macroevolution. Choosing between the contrasting 'discontinuity' and 'ethology' models will require next-generation sequencing of nuclear genomes plus ordination of corresponding morphometric matrices, seeking the crucial distinction between retained ancestral polymorphism-consistent with lineage divergence-and polymorphisms reflecting gene flow through 'hybridization'-more consistent with lineage convergence.
Collapse
|
45
|
Wei N, Pérez-Escobar OA, Musili PM, Huang WC, Yang JB, Hu AQ, Hu GW, Grace OM, Wang QF. Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region. FRONTIERS IN PLANT SCIENCE 2021; 12:712064. [PMID: 34421963 PMCID: PMC8372406 DOI: 10.3389/fpls.2021.712064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 05/09/2023]
Abstract
With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.
Collapse
Affiliation(s)
- Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Paul M. Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Wei-Chang Huang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Olwen M. Grace
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- *Correspondence: Olwen M. Grace,
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Qing-Feng Wang,
| |
Collapse
|
46
|
Schneider JV, Paule J, Jungcurt T, Cardoso D, Amorim AM, Berberich T, Zizka G. Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:638650. [PMID: 33613613 PMCID: PMC7890083 DOI: 10.3389/fpls.2021.638650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family's backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family's species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
Collapse
Affiliation(s)
- Julio V. Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Entomology III, Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Tanja Jungcurt
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - André Márcio Amorim
- Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
- Herbário André Maurício Vieira de Carvalho, CEPEC, CEPLAC, Itabuna, Brazil
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Lab-Center, Frankfurt am Main, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- *Correspondence: Georg Zizka, ;
| |
Collapse
|
47
|
Zhang CY, Liu TJ, Mo XL, Huang HR, Yao G, Li JR, Ge XJ, Yan HF. Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae). PLANTS 2020; 9:plants9111497. [PMID: 33167549 PMCID: PMC7694494 DOI: 10.3390/plants9111497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/06/2023]
Abstract
Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.
Collapse
Affiliation(s)
- Cai-Yun Zhang
- Guangdong Food and Drug Vocational College, Guangzhou 510520, China; (C.-Y.Z.); (X.-L.M.)
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Correspondence:
| | - Xiao-Lu Mo
- Guangdong Food and Drug Vocational College, Guangzhou 510520, China; (C.-Y.Z.); (X.-L.M.)
| | - Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gang Yao
- South China Limestone Plants Research Centre, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China;
| | - Jian-Rong Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
48
|
Xiao TW, Xu Y, Jin L, Liu TJ, Yan HF, Ge XJ. Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PeerJ 2020; 8:e10155. [PMID: 33088627 PMCID: PMC7568859 DOI: 10.7717/peerj.10155] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.
Collapse
Affiliation(s)
- Tian-Wen Xiao
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lu Jin
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tong-Jian Liu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Hai-Fei Yan
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| |
Collapse
|
49
|
Li L, Wang S, Wang H, Sahu SK, Marin B, Li H, Xu Y, Liang H, Li Z, Cheng S, Reder T, Çebi Z, Wittek S, Petersen M, Melkonian B, Du H, Yang H, Wang J, Wong GKS, Xu X, Liu X, Van de Peer Y, Melkonian M, Liu H. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nat Ecol Evol 2020; 4:1220-1231. [PMID: 32572216 PMCID: PMC7455551 DOI: 10.1038/s41559-020-1221-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 05/12/2020] [Indexed: 12/31/2022]
Abstract
Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.
Collapse
Affiliation(s)
- Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Birger Marin
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Haoyuan Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Tanja Reder
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Zehra Çebi
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Morten Petersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany.
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
50
|
Zhang X, Sun Y, Landis JB, Lv Z, Shen J, Zhang H, Lin N, Li L, Sun J, Deng T, Sun H, Wang H. Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes. BMC PLANT BIOLOGY 2020; 20:340. [PMID: 32680458 PMCID: PMC7368685 DOI: 10.1186/s12870-020-02518-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied. RESULTS We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one (matK) of the three (matK, ndhB and rbcL) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection. CONCLUSIONS Overall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.
Collapse
Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92507, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
| | - Zhenyu Lv
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jun Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiao Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| |
Collapse
|