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Frazão A, Thode VA, Lohmann LG. Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae). Sci Rep 2023; 13:12469. [PMID: 37528152 PMCID: PMC10394017 DOI: 10.1038/s41598-023-39403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Species of Tanaecium (Bignonieae, Bignoniaceae) are lianas distributed in the Neotropics and centered in the Amazon. Members of the genus exhibit exceptionally diverse flower morphology and pollination systems. Here, we sequenced, assembled, and annotated 12 complete and four partial chloroplast genomes representing 15 Tanaecium species and more than 70% of the known diversity in the genus. Gene content and order were similar in all species of Tanaecium studied, with genome sizes ranging between 158,470 and 160,935 bp. Tanaecium chloroplast genomes have 137 genes, including 80-81 protein-coding genes, 37 tRNA genes, and four rRNA genes. No rearrangements were found in Tanaecium plastomes, but two different patterns of boundaries between regions were recovered. Tanaecium plastomes show nucleotide variability, although only rpoA was hypervariable. Multiple SSRs and repeat regions were detected, and eight genes were found to have signatures of positive selection. Phylogeny reconstruction using 15 Tanaecium plastomes resulted in a strongly supported topology, elucidating several relationships not recovered previously and bringing new insights into the evolution of the genus.
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Affiliation(s)
- Annelise Frazão
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
- Departamento de Biodiversidade e Bioestatística, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil.
| | - Verônica A Thode
- Programa de Pós-Graduação em Botânica, Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lúcia G Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, USA.
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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.
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Out of chaos: Phylogenomics of Asian Sonerileae. Mol Phylogenet Evol 2022; 175:107581. [PMID: 35810973 DOI: 10.1016/j.ympev.2022.107581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/22/2022]
Abstract
Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.
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Huang Y, Li J, Yang Z, An W, Xie C, Liu S, Zheng X. Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species. BMC PLANT BIOLOGY 2022; 22:253. [PMID: 35606691 PMCID: PMC9125854 DOI: 10.1186/s12870-022-03643-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species. RESULTS The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus. CONCLUSION The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.
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Affiliation(s)
- Yuying Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Jing Li
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510410, China
| | - Zerui Yang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Wenli An
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Chunzhu Xie
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Shanshan Liu
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuangdong Road, Higher Education Mega Center, Panyu District, Guangzhou, Guangdong, China.
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Literman RA, Ott BM, Wen J, Grauke LJ, Schwartz RS, Handy SM. Reference-free discovery of nuclear SNPs permits accurate, sensitive identification of Carya (hickory) species and hybrids. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11455. [PMID: 35228913 PMCID: PMC8861591 DOI: 10.1002/aps3.11455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
PREMISE DNA-based species identification is critical when morphological identification is restricted, but DNA-based identification pipelines typically rely on the ability to compare homologous sequence data across species. Because many clades lack robust genomic resources, we present here a bioinformatics pipeline capable of generating genome-wide single-nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data. METHODS Using the SISRS bioinformatics pipeline, we generated de novo ortholog data for the genus Carya, isolating sites where genetic variation was restricted to a single Carya species (i.e., species-informative SNPs). We leveraged these SNPs to identify both full-species and hybrid Carya specimens, even at very low sequencing depths. RESULTS We identified between 46,000 and 476,000 species-identifying SNPs for each of eight diploid Carya species, and all species identifications were concordant with the species of record. For all putative F1 hybrid specimens, both parental species were correctly identified in all cases, and more punctate patterns of introgression were detectable in more cryptic crosses. DISCUSSION Bioinformatics pipelines that use only short-read sequencing data provide vital new tools enabling rapid expansion of DNA identification assays for model and non-model clades alike.
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Affiliation(s)
- Robert A. Literman
- Office of Regulatory Science, Center for Food Safety and Applied NutritionU.S. Food and Drug AdministrationCollege ParkMarylandUSA
| | - Brittany M. Ott
- Office of Food Additive Safety, Center for Food Safety and Applied NutritionU.S. Food and Drug AdministrationCollege ParkMarylandUSA
| | - Jun Wen
- Department of Botany, National Museum of Natural HistorySmithsonian InstitutionWashington, D.C.USA
| | - L. J. Grauke
- United States Department of Agriculture (USDA)–Agricultural Research Service Pecan Breeding and GeneticsSomervilleTexasUSA
| | - Rachel S. Schwartz
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Sara M. Handy
- Office of Regulatory Science, Center for Food Safety and Applied NutritionU.S. Food and Drug AdministrationCollege ParkMarylandUSA
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Maurin O, Anest A, Bellot S, Biffin E, Brewer G, Charles-Dominique T, Cowan RS, Dodsworth S, Epitawalage N, Gallego B, Giaretta A, Goldenberg R, Gonçalves DJP, Graham S, Hoch P, Mazine F, Low YW, McGinnie C, Michelangeli FA, Morris S, Penneys DS, Pérez Escobar OA, Pillon Y, Pokorny L, Shimizu G, Staggemeier VG, Thornhill AH, Tomlinson KW, Turner IM, Vasconcelos T, Wilson PG, Zuntini AR, Baker WJ, Forest F, Lucas E. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. AMERICAN JOURNAL OF BOTANY 2021; 108:1087-1111. [PMID: 34297852 DOI: 10.1002/ajb2.1699] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
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Affiliation(s)
- Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Artemis Anest
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Edward Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Tristan Charles-Dominique
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil
| | - Renato Goldenberg
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | | | - Peter Hoch
- Missouri Botanical Garden, St. Louis, MO, 63110, USA
| | - Fiorella Mazine
- Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil
| | - Yee Wen Low
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | | | - Fabián A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | | | - Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Gustavo Shimizu
- Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil
| | - Andrew H Thornhill
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Ian M Turner
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Peter G Wilson
- Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Eve Lucas
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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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.
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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
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Zhang XF, Landis JB, Wang HX, Zhu ZX, Wang HF. Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. BMC PLANT BIOLOGY 2021; 21:219. [PMID: 33992095 PMCID: PMC8122561 DOI: 10.1186/s12870-021-02985-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. RESULTS A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214-171,315 bp and exhibit a typical four part structure. The IR region is between 23,901-36,747 bp, with the large single copy region spanning 83,691-91,249 bp and the small single copy region spanning 11,150-19,703 bp. In total, 123-133 genes are present in the chloroplasts including 77-81 protein coding genes, four rRNA genes and 30-31 tRNA genes. The GC content was 36.9-38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7-37.3%, 30.6-36.8% and 39.7-43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88-114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50-118.62 Ma). CONCLUSIONS The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.
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Affiliation(s)
- Xiao-Feng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Hong-Xin Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
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Zeng SJ, Xu YC, Wang GT, Jia P, Cui DF. Tigridiopalma exalata, a new and endangered species of Melastomataceae from China. PHYTOKEYS 2021; 176:33-42. [PMID: 33958937 PMCID: PMC8065001 DOI: 10.3897/phytokeys.176.63619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
A new species of the genus Tigridiopalma, formerly considered monotypic, is here described as T. exalata and illustrated based on molecular and morphological evidence. It is morphologically similar to T. magnifica in having a short stem, huge basal leaves, scorpioid cymes, and 5-merous flowers, but differs in having ribbed and pale yellow puberulent petioles, purple petals with a small white apical patch, connectives of longer stamens with a distinct dorsal short spur at their base, and wingless capsules. Due to the restricted distribution, small populations and horticultural potential of this new species, it should be categorized as an Endangered species (EN).
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Affiliation(s)
- Si-Jin Zeng
- College of Forestry and Landscape Architecture/Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Ye-Chun Xu
- Environmental Horticulture Research Institute/Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Gang-Tao Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Jia
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510420, Guangdong, China
| | - Da-Fang Cui
- College of Forestry and Landscape Architecture/Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, Guangdong, China
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10
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Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR. Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PeerJ 2021; 9:e10886. [PMID: 33665028 PMCID: PMC7912680 DOI: 10.7717/peerj.10886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.
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Affiliation(s)
- Benoit Loeuille
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Verônica Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carolina Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States of America
| | - Sonia Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - José Rubens Pirani
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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11
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Lima DF, Goldenberg R, Forest F, Cowan RS, Lucas EJ. Phylogeny and biogeography of Myrcia sect. Aguava (Myrtaceae, Myrteae) based on phylogenomic and Sanger data provide evidence for a Cerrado origin and geographically structured clades. Mol Phylogenet Evol 2020; 157:107043. [PMID: 33346112 DOI: 10.1016/j.ympev.2020.107043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/18/2022]
Abstract
Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed.
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Affiliation(s)
- Duane F Lima
- Programa de Pós-Graduação em Biologia Vegetal, IB, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil.
| | - Renato Goldenberg
- Departamento de Botânica, SCB, Universidade Federal do Paraná, 81531-970 Curitiba, PR, Brazil
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Robyn S Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Eve J Lucas
- Herbarium, Royal Botanic Gardens, Kew, TW9 3AB Richmond, Surrey, United Kingdom
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12
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Köhler M, Reginato M, Souza-Chies TT, Majure LC. Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies. FRONTIERS IN PLANT SCIENCE 2020; 11:729. [PMID: 32636853 PMCID: PMC7317007 DOI: 10.3389/fpls.2020.00729] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 05/22/2023]
Abstract
Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.
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Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Florida Museum of Natural History, University of Florida Herbarium (FLAS), Gainesville, FL, United States
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Lucas C Majure
- Florida Museum of Natural History, University of Florida Herbarium (FLAS), Gainesville, FL, United States
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, United States
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13
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Reginato M, Vasconcelos TNC, Kriebel R, Simões AO. Is dispersal mode a driver of diversification and geographical distribution in the tropical plant family Melastomataceae? Mol Phylogenet Evol 2020; 148:106815. [PMID: 32278864 DOI: 10.1016/j.ympev.2020.106815] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022]
Abstract
Species of plants with different life history strategies may differ in their seed dispersal mechanisms, impacting their distribution and diversification patterns. Shorter or longer distance dispersal is favored by different dispersal modes, facilitating (or constraining) population isolation, which can, in turn, impact speciation and species range sizes. While these associations are intuitive, few studies have explicitly tested these hypotheses for large clades of angiosperms. The plant family Melastomataceae is found on disparate habitats with different dispersal modes, representing a good model to address these questions. In this study, we reconstruct the phylogeny of Melastomataceae and gather data on their dispersal mode and range size to test the impact of dispersal mode on diversification and range size evolution. We found that abiotic dispersal is ancestral in the family, while biotic dispersal evolved multiple times. Species richness distribution is very similar across dispersal modes, although abiotically dispersed species tend to be relatively more diverse in seasonal environments. Range sizes across dispersal modes are not significantly different, although biotically dispersed species have slightly wider distributions. Model comparisons indicate that factors other than dispersal mode might have driven diversification heterogeneity. We did not find evidence for the role of dispersal mode driving diversification rates or range size in the Melastomataceae, suggesting a complex macroevolutionary scenario for this diverse angiosperm family. The bulk of changes to biotic dispersal coinciding with an increase in passerine diversification suggests a possible "past" key innovation in Melastomataceae. Future studies should investigate the role of other diversification drivers in the family and the relatively higher diversity of abiotically dispersed species in open habitats.
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Affiliation(s)
- Marcelo Reginato
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Thais N C Vasconcelos
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - André Olmos Simões
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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14
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An W, Li J, Yang Z, Huang Y, Huang S, Zheng X. Characteristics analysis of the complete Wurfbainia villosa chloroplast genome. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:747-758. [PMID: 32255937 PMCID: PMC7113360 DOI: 10.1007/s12298-019-00748-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/25/2019] [Accepted: 12/13/2019] [Indexed: 05/05/2023]
Abstract
Wurfbainia villosa, which belongs to the huge family Zingiberaceae, is used in the clinic for the treatment of spleen and stomach diseases in southern China. The complete chloroplast genome of W. villosa was sequenced and analyzed using next-generation sequencing technology in the present work. The results showed that the W. villosa chloroplast genome is a circular molecule with 163,608 bp in length. It harbors a pair of inverted repeat regions (IRa and IRb) of 29,820 bp in length, which separate the large single copy (LSC, 88,680 bp) region and the small single copy (SSC, 15,288 bp) region. After annotation, 134 genes were identified in this plastome in total, comprising of 87 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes and one pseudogene (ycf1). Codon usage, RNA editing sites and single/long sequence repeats were investigated to understand the structural characteristics of the W. villosa chloroplast genome. Furthermore, IR contraction and expansion were analyzed by comparison of complete chloroplast genomes of W. villosa and four other Zingiberaceae species. Finally, a phylogeny study based on the chloroplast genome of W. villosa, along with that of 15 different species, was conducted to further investigate the relationship among these lineages. Overally, our results represented the first insight into the chloroplast genome of W. villosa, and could serve as a significant reference for species identification, genetic diversity analysis and phylogenetic research between W. villosa and other species within Zingiberaceae.
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Affiliation(s)
- Wenli An
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Jing Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510410 Guangdong China
- Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510410 China
| | - Zerui Yang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Yuying Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
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15
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Zhou Q, Lin CW, Ng WL, Dai J, Denda T, Zhou R, Liu Y. Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae. FRONTIERS IN PLANT SCIENCE 2019; 10:1477. [PMID: 31824528 PMCID: PMC6881482 DOI: 10.3389/fpls.2019.01477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/24/2019] [Indexed: 05/31/2023]
Abstract
Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.
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Affiliation(s)
- Qiujie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Che-Wei Lin
- Division of Botanical Garden, Herbarium of Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Malaysia
| | - Jinhong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tetsuo Denda
- Laboratory of Ecology and Systematics, Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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16
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Wen ZY, Zeng SJ, Han W, Chen B, Peng DH. The complete chloroplast genome sequence of Blastus pauciflorus (Melastomataceae). Mitochondrial DNA B Resour 2019; 4:3854-3855. [PMID: 33366219 PMCID: PMC7707767 DOI: 10.1080/23802359.2019.1687035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/26/2019] [Indexed: 11/02/2022] Open
Abstract
Blastus pauciflorus, a shrub endemic to Hong Kong and Guangdong, south China, growing on low-altitude hillsides, under the forest. The species is controversial in classification. Herein, we report the complete chloroplast genome sequence assembled from Illumina pair-end sequencing data, with aims to resolve its relationship with the related species. The complete chloroplast genome was 155,983 bp in length, includes two inverted repeat regions (IRs) of 26,716 bp each, which were separated by a large single copy region (LSC) 86,101 bp and a small single copy region (SSC) 16,450 bp. The chloroplast genome contained 129 genes, including 82 protein-coding genes, 2 pseudogenes, 37 tRNA genes and 8 rRNA genes. The overall GC content in the chloroplast genome of B. pauciflorus was 37.0%. Phylogenetic analysis showed that B. pauciflorus is closed to B. cochinchinensis.
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Affiliation(s)
- Zhen Ying Wen
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Si Jin Zeng
- South China Agricultural University, Guangzhou, China
- The National Orchid Conservation Center of China, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Wenchao Han
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bin Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dong Hui Peng
- Fujian Agriculture and Forestry University, Fuzhou, China
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17
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Wen Z, Zeng S, Li T, Zhang G, Peng D. The complete chloroplast genome sequence of monotypic Cyphotheca (Melastomataceae), an endemic genus in China. Mitochondrial DNA B Resour 2019; 4:2295-2296. [PMID: 33365512 PMCID: PMC7687601 DOI: 10.1080/23802359.2019.1627932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/17/2019] [Indexed: 11/23/2022] Open
Abstract
Cyphotheca, a shrub narrowly endemic to Yunnan, southwest China, is a monotypic genus of Sonerileae in Melastomataceae. The species, Cyphotheca montana, is dwindling and is listed as 'Near Threatened (NT)' by IUCN Red List of China. Herein, we report the complete chloroplast genome (cpDNA) sequence assembled from Illumina pair-end sequencing data. The complete chloroplast genome was 156,424 bp in length, which includes two inverted repeat regions (IRs) of 26,776 bp each, which were separated by a large single copy region (LSC) 85,900 bp and a small single copy region (SSC) 16,972 bp. The chloroplast genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content in the chloroplast genome of C. montana was 37.0%. The phylogenomic analysis showed that C. montana is sister to Barthea barthei.
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Affiliation(s)
- Zhenying Wen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sijin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzen, China
- College of Forestry and Landscape Architecture, South China Limestone Plants Research Center, South China Agricultural University, Guangzhou, China
| | - Tingzhang Li
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzen, China
| | - Guoqiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzen, China
| | - Donghui Peng
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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18
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Zhang W, Wen Z, Zeng S, Luo L, Peng D. Characterization of the complete chloroplast genome sequence of Blastus cochinchinensis (Melastomataceae). Mitochondrial DNA B Resour 2019; 4:2185-2186. [PMID: 33365466 PMCID: PMC7687533 DOI: 10.1080/23802359.2019.1624639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 05/17/2019] [Indexed: 11/06/2022] Open
Abstract
Blastus Lour. belongs to tribe Sonerileae (Melastomataceae), comprising about 18 species worldwide. Herein, we presented, assembled, and annotated the first complete chloroplast genome of Blastus (B. cochinchinensis). The complete chloroplast genome (cp) size of B. cochinchinensis was 156,005 bp in length, containing a pair of 26,812 bp inverted repeat (IR) regions, which were separated by a large single-copy region (LSC) 85,926 bp and a small single-copy (SSC) region 16,455 bp. The overall GC content of the genome was 37.0%. The whole genome contained 129 unique genes, including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that B. cochinchinens was sister to Barthea barthei. The present study provided B. cochinchinensis genomic information that may be found useful in conservation and molecular phylogenetic studies on Blastus.
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Affiliation(s)
- Wenchun Zhang
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhenying Wen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Sijin Zeng
- College of Forestry and Landscape Architecture, South China Limestone Plants Research Center, South China Agricultural University, Guangzhou, Guangdong, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Liang Luo
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Donghui Peng
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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19
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Zheng X, Ren C, Huang S, Li J, Zhao Y. Structure and features of the complete chloroplast genome of Melastoma dodecandrum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1043-1054. [PMID: 31404219 PMCID: PMC6656900 DOI: 10.1007/s12298-019-00651-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/27/2018] [Accepted: 02/19/2019] [Indexed: 05/29/2023]
Abstract
Melastoma dodecandrum, the only creeping species in the Melastoma genus, serves as a medicinal herb in southeast China. It belongs to the huge family Melastomataceae, which contains over 5000 species worldwide. In this study, we used next-generation sequencing to determine the complete chloroplast genome sequences of M. dodecandrum, which is a circular molecule of 156,611 bp in length. After annotation, we identified 131 putative genes in total, comprised of 85 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Genome structure, GC content, repeat sequences and codon usage were investigated to gain a comprehensive understanding of this genome. Furthermore, we conducted comparative genome analyses between the M. dodecandrum genome and that of four other Melastomataceae species. Additionally, a phylogenetic analysis was performed based on available chloroplast genomes of Melastomataceae species and several Myrtaceae species, revealing the taxonomic relationships between M. dodecandrum and related species. In conclusion, our study represents the first look into the complete chloroplast genome of M. dodecandrum, providing abundant information for further studies such as species identification, taxonomy and phylogenetic resolution of Melastomataceae species.
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Affiliation(s)
- Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Changwei Ren
- Department of Cardiovascular Surgery Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029 China
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Jing Li
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Ying Zhao
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
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20
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Gu C, Ma L, Wu Z, Chen K, Wang Y. Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales. BMC PLANT BIOLOGY 2019; 19:281. [PMID: 31242865 PMCID: PMC6595698 DOI: 10.1186/s12870-019-1870-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species. RESULTS We reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049 bp to 160,769 bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211-332 simple sequence repeats (SSRs) in six categories and 7-27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales. CONCLUSIONS The study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.
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Affiliation(s)
- Cuihua Gu
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Li Ma
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kai Chen
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yixiang Wang
- School of Environment and Resources, Zhejiang A&F University, Hangzhou, 311300, China
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21
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Zheng T, Lin Y, Wang L, Lin Q, Lin X, Chen Z, Lin Z. De novo Assembly and Characterization of the Floral Transcriptomes of Two Varieties of Melastoma malabathricum. Front Genet 2019; 10:521. [PMID: 31275350 PMCID: PMC6594232 DOI: 10.3389/fgene.2019.00521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 05/13/2019] [Indexed: 11/24/2022] Open
Abstract
Melastoma malabathricum is an important medicinal and landscape plant that is globally distributed in temperate and subtropical regions. However, available genomic information for the entire Melastomataceae family is notably limited. In view of the application potential of floral parts in secondary metabolite extraction, we characterized for the first time the floral transcriptomes of two key M. malabathricum varieties, purple variety and white variety. Our transcriptome assembly generated 52,498 and 49,380 unigenes with an N50 of 1,906 and 1,929 bases for the purple and white varieties, respectively. Comparative analysis of two transcriptomes demonstrated that they are highly similar but also highlighted genes that are presumably lineage specific, which explains the phenotypes of each variety. Additionally, a shared transcriptional signature across the floral developmental stages was identified in both M. malabathricum varieties; this signature included pathways related to secondary metabolite synthesis, plant hormone signaling and production, energy homeostasis and nutrient assimilation pathways, and cellular proliferation. The expression levels of flavonoid accumulation and candidate flavonoid biosynthesis-related genes in M. malabathricum flower development stages validated the transcriptome findings. The transcriptome data presented in this study will serve as a valuable resource for future work on the exploitation of M. malabathricum and other related species. The gene expression dynamics during flower development will facilitate the discovery of lineage-specific genes associated with phenotypic characteristics and will elucidate the mechanism of the ontogeny of individual flower types.
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Affiliation(s)
- Tao Zheng
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Yihua Lin
- Fujian Institute of Tropical Crops, Zhangzhou, China.,Institute of Oceanography, Minjiang University, Fuzhou, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Longping Wang
- Fujian Institute of Tropical Crops, Zhangzhou, China.,Xiamen Forest Quarantine and Prevention Station, Xiamen Greening Administration Center, Xiamen, China
| | - Qiujin Lin
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Xiuxiang Lin
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Zhendong Chen
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Zhenyue Lin
- Institute of Oceanography, Minjiang University, Fuzhou, China
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22
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Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome. PLANTS 2019; 8:plants8040089. [PMID: 30987338 PMCID: PMC6524380 DOI: 10.3390/plants8040089] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 11/16/2022]
Abstract
In the last decade, several studies have relied on a small number of plastid genomes to deduce deep phylogenetic relationships in the species-rich Myrtaceae. Nevertheless, the plastome of Rhodomyrtus tomentosa, an important representative plant of the Rhodomyrtus (DC.) genera, has not yet been reported yet. Here, we sequenced and analyzed the complete chloroplast (CP) genome of R. tomentosa, which is a 156,129-bp-long circular molecule with 37.1% GC content. This CP genome displays a typical quadripartite structure with two inverted repeats (IRa and IRb), of 25,824 bp each, that are separated by a small single copy region (SSC, 18,183 bp) and one large single copy region (LSC, 86,298 bp). The CP genome encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes and three pseudogenes (ycf1, rps19, ndhF). A considerable number of protein-coding genes have a universal ATG start codon, except for psbL and ndhD. Premature termination codons (PTCs) were found in one protein-coding gene, namely atpE, which is rarely reported in the CP genome of plants. Phylogenetic analysis revealed that R. tomentosa has a sister relationship with Eugenia uniflora and Psidium guajava. In conclusion, this study identified unique characteristics of the R. tomentosa CP genome providing valuable information for further investigations on species identification and the phylogenetic evolution between R. tomentosa and related species.
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23
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Yang Z, Huang Y, An W, Zheng X, Huang S, Liang L. Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill. PLANTS (BASEL, SWITZERLAND) 2019; 8:E87. [PMID: 30987216 PMCID: PMC6524360 DOI: 10.3390/plants8040087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 01/01/2023]
Abstract
Lycium chinense Mill, an important Chinese herbal medicine, is widely used as a dietary supplement and food. Here the chloroplast (CP) genome of L. chinense was sequenced and analyzed, revealing a size of 155,756 bp and with a 37.8% GC content. The L. chinense CP genome comprises a large single copy region (LSC) of 86,595 bp and a small single copy region (SSC) of 18,209 bp, and two inverted repeat regions (IRa and IRb) of 25,476 bp separated by the single copy regions. The genome encodes 114 genes, 16 of which are duplicated. Most of the 85 protein-coding genes (CDS) had standard ATG start codons, while 3 genes including rps12, psbL and ndhD had abnormal start codons (ACT and ACG). In addition, a strong A/T bias was found in the majority of simple sequence repeats (SSRs) detected in the CP genome. Analysis of the phylogenetic relationships among 16 species revealed that L. chinense is a sister taxon to Lycium barbarum. Overall, the complete sequence and annotation of the L. chinense CP genome provides valuable genetic information to facilitate precise understanding of the taxonomy, species and phylogenetic evolution of the Solanaceae family.
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Affiliation(s)
- Zerui Yang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Yuying Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Wenli An
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Lingling Liang
- Pharmaceutical School, YouJiang Medical University for Nationalities, Baise 533000, China.
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24
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Tan G, Han B, Wang Y, Li Z, Zhao Y, Luo S, Liu X, Liu Y, Zhou Q. The complete chloroplast genome of Blastus auriculatus (Melastomataceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Guangwen Tan
- Pubang Landscape Architecture Co.,Ltd, Guangzhou, China
| | - Bingqian Han
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yongqi Wang
- Pubang Landscape Architecture Co.,Ltd, Guangzhou, China
| | - Zihua Li
- Pubang Landscape Architecture Co.,Ltd, Guangzhou, China
| | - Yangyang Zhao
- Pubang Landscape Architecture Co.,Ltd, Guangzhou, China
| | - Shuai Luo
- Pubang Landscape Architecture Co.,Ltd, Guangzhou, China
| | - Xiaozhou Liu
- Pubang Landscape Architecture Co.,Ltd, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiujie Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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25
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Gonçalves DJP, Versiane AFA. The complete plastome sequence of Microlicia cogniauxiana R. Romero (Melastomataceae): an endemic species from an endangered biome. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1617058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Deise J. P. Gonçalves
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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26
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Thode VA, Lohmann LG. Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:796. [PMID: 31275342 PMCID: PMC6594259 DOI: 10.3389/fpls.2019.00796] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/03/2019] [Indexed: 05/13/2023]
Abstract
Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum. We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD, or within petB). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum. The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.
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27
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Contrasting patterns of taxonomic, phylogenetic and functional variation along a Costa Rican altitudinal gradient in the plant family Melastomataceae. JOURNAL OF TROPICAL ECOLOGY 2018. [DOI: 10.1017/s0266467418000172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract:The functional composition of plant communities in montane regions has been studied for decades, and most recent analyses find that environmentally favourable landscapes at lower altitudes tend to be dominated by species with resource-acquisitive traits, while more resource-conservative taxa dominate higher-altitude communities. However, it is unclear the extent to which this pattern is driven by co-gradient variation within clades or changes in clade representation across the gradient. To test for co-gradient variation, species composition, phylogenetic structure and functional traits were quantified for 97 species within the plant family Melastomataceae at five locations across a 2500-m altitudinal gradient along Volcán Barva in Costa Rica. Average melastome leaf force to punch, specific leaf area and leaf size vary with altitude, while four other functional traits do not. Taxonomic dissimilarity between communities was correlated with altitudinal difference, while phylogenetic dissimilarity was correlated with altitudinal dissimilarity only when measured with a metric that emphasizes shallow turnover of the tips of the phylogeny. These results highlight how species turnover may be more pronounced than functional or phylogenetic variation along altitudinal gradients. In addition, these results highlight the conservation value of lowland tropical forests, which here harbour a disproportionate amount of phylogenetic and functional diversity.
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28
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Fu CN, Li HT, Milne R, Zhang T, Ma PF, Yang J, Li DZ, Gao LM. Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution. BMC Genomics 2017; 18:956. [PMID: 29216844 PMCID: PMC5721659 DOI: 10.1186/s12864-017-4319-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/21/2017] [Indexed: 12/03/2022] Open
Abstract
Background The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. Results All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859–26,451 bp) separated by a large single-copy region (86,089–87,835 bp) and a small single-copy region (18,250–18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified. Conclusions Phylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants. Electronic supplementary material The online version of this article (10.1186/s12864-017-4319-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao-Nan Fu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Edinburgh, Scotland, EH9 3JH, UK
| | - Ting Zhang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Yang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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29
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He X, Zhou Y, Cai Y, Chen Z, Wu W, Zhou R, Ng WL. The complete chloroplast genome sequence of Barthea barthei (Melastomataceae), a shrub endemic to southern China. Mitochondrial DNA B Resour 2017; 2:810-811. [PMID: 33473991 PMCID: PMC7799996 DOI: 10.1080/23802359.2017.1403868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/08/2017] [Indexed: 12/02/2022] Open
Abstract
The plant genus Barthea is monotypic, comprising of only a single species (Barthea barthei), and is endemic to southern China. In this study, we report the complete chloroplast genome of B. barthei, assembled from whole-genome high-throughput sequencing data, as a resource for future studies on the taxonomy and evolution of Barthea. The chloroplast genome was 155,951 bp in length, with a large single-copy (LSC) region of 85,882 bp, a small single-copy (SSC) region of 16,445 bp, separated by two inverted repeat (IR) regions of 26,812 bp each. It was predicted to contain a total of 130 genes, with an overall GC content of 36.99%. Phylogenetic analysis placed B. barthei closest to Opisthocentra sp. in Melastomataceae.
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Affiliation(s)
- Xuejiao He
- Fujian Institute of Tropical Crops, Zhangzhou, Fujian, China
| | - Yubing Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yacheng Cai
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhendong Chen
- Fujian Institute of Tropical Crops, Zhangzhou, Fujian, China
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Lun Ng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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30
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Zhou Q, Ng WL, Wu W, Zhou R, Liu Y. Characterization of the complete chloroplast genome sequence of Tigridiopalma magnifica (Melastomataceae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0856-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Ng WL, Cai Y, Wu W, Zhou R. The complete chloroplast genome sequence of Melastoma candidum (Melastomataceae). Mitochondrial DNA B Resour 2017; 2:242-243. [PMID: 33473785 PMCID: PMC7800422 DOI: 10.1080/23802359.2017.1318680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The plant genus Melastoma is comprised of members estimated to have formed through recent species radiation. Natural hybridization among member species further complicates taxonomy within the genus. Herein, we report the complete chloroplast genome of M. candidum, assembled from partial data obtained from a parallel whole-genome Illumina paired-end sequencing effort on the species. The chloroplast genome was 156,682 bp in length, with a large single-copy (LSC) region of 86,084 bp, a small single-copy (SSC) region of 17,094 bp, separated by two inverted repeat (IR) regions of 26,752 bp each. It was predicted to contain a total of 129 genes, with an overall GC content of 37.17%. Phylogenetic analysis placed M. candidum in the same clade as species within the Melastomeae tribe of Melastomataceae.
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Affiliation(s)
- Wei Lun Ng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yacheng Cai
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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32
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Fonseca LHM, Lohmann LG. Plastome Rearrangements in the " Adenocalymma-Neojobertia" Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications. FRONTIERS IN PLANT SCIENCE 2017; 8:1875. [PMID: 29163600 PMCID: PMC5672021 DOI: 10.3389/fpls.2017.01875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 10/16/2017] [Indexed: 05/02/2023]
Abstract
The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes. Plastomes were assembled using selected plastid reads and de novo approach with SPAdes. The 10 assembled genomes were analyzed in a phylogenetic context using five different partition schemes: (1) 91 protein-coding genes ("coding"); (2) 76 introns and spacers with alignment manually edited ("non-coding edited"); (3) 76 non-coding regions with poorly aligned regions removed using T-Coffee ("non-coding filtered"); (4) 91 coding regions plus 76 non-coding regions edited ("coding + non-coding edited"); and, (5) 91 protein-coding regions plus the 76 filtered non-coding regions ("coding + non-coding filtered"). Fragmented regions were aligned using Mafft. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Criteria (BC). The analyses of the individual plastomes consistently recovered an expansion of the Inverted Repeated (IRs) regions and a compression of the Small Single Copy (SSC) region. Major genomic translocations were observed at the Large Single Copy (LSC) and IRs. ML phylogenetic analyses of the individual datasets led to the same topology, with the exception of the analysis of the "non-coding filtered" dataset. Overall, relationships were strongly supported, with the highest support values obtained through the analysis of the "coding + non-coding edited" dataset. Four regions at the LSC, SSC, and IR were selected for primer development. The "Adenocalymma-Neojobertia" clade shows an unusual pattern of plastid structure variation, including four major genomic translocations. These rearrangements challenge the current view of conserved plastid genome architecture in terms of gene order. It also complicates both genomic assemblies using reference genomes and sequence alignments using whole plastomes. Therefore, strategies that employ de novo assemblies and manual evaluation of sequence alignments are required to prevent assembly and alignment errors.
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