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Ling C, Zhang M, Ma W, Liu M. The complete sequence of chloroplast genome of Baeckea frutescens Linaeus 1753 (Myrtoideae), a traditional folk medicinal plant. Mitochondrial DNA B Resour 2024; 9:1384-1388. [PMID: 39381366 PMCID: PMC11459836 DOI: 10.1080/23802359.2024.2412239] [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: 07/11/2024] [Accepted: 09/28/2024] [Indexed: 10/10/2024] Open
Abstract
Baeckea frutescens Linaeus 1753, as a traditional folk medicine in South East Asia, possesses sesquiterpenes, phloroglucinols, chromones, and essential oil, and is utilized for traditional Chinese medicinal purposes. The genetic diversity of the plant must be better understood, considering its significance. The complete chloroplast (cp) genome of B. frutescens was sequenced and assembled by using Illumina paired-end data, marking a significant advancement toward comprehending its genetic composition. The complete cp genome is 158,939 bp in length and contains 128 genes, consisting of 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analyses indicated that B. frutescens and other the 13 were clustered to the family of Myrtaceae. These findings are crucial for the conservation and utilization of this important plant species. Additionally, they underscore the potential for future research on the evolution and preservation of B. frutescens, which could be advantageous in pharmaceutical applications.
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Affiliation(s)
- Chengcheng Ling
- College of Food and Bioengineering, Bengbu University, Bengbu, China
| | - Menglei Zhang
- College of Food and Bioengineering, Bengbu University, Bengbu, China
| | - Wenwen Ma
- College of Food and Bioengineering, Bengbu University, Bengbu, China
| | - Menyu Liu
- College of Food and Bioengineering, Bengbu University, Bengbu, China
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Hai Y, Qian Y, Yang M, Zhang Y, Xu H, Yang Y, Xia C. The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species. Sci Rep 2024; 14:13945. [PMID: 38886540 PMCID: PMC11183227 DOI: 10.1038/s41598-024-64896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129-134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.
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Affiliation(s)
- Yonglin Hai
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yan Qian
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Meihua Yang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yue Zhang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Huimei Xu
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yongcheng Yang
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
| | - Conglong Xia
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
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Cao Z, Qu Y, Song Y, Xin P. Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae). Gene 2024; 907:148259. [PMID: 38346458 DOI: 10.1016/j.gene.2024.148259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
The genus Caryodaphnopsis, a member of the Lauraceae family, is characterized by seeds that are rich in oil, as well as highly exploitable fruits and wood. The Asian taxa within this genus exhibit complex morphological variations, posing challenges to their accurate classification and impeding their effective use and development as a resource. In this study, we sequenced the chloroplast genomes of 31 individuals representing nine Asian taxa within the Caryodaphnopsis genus. Our primary objectives were to reveal structural variations in these chloroplast genomes through comparative analyses and to infer the species' phylogenetic relationships. Our findings revealed that all chloroplast genomes had a tetrad structure, ranged in length from 148,828 to 154,946 bp, and harbored 128-131 genes. Notably, contraction of the IR region led to the absence of some genes in eight taxa. A comprehensive analysis identified 1267 long repetitive sequences and 2176 SSRs, 286 SNPs, and 135 indels across the 31 chloroplast genomes. The Ka/Ks ratio analysis indicated potential positive selection on the matK, rpl22, and rpoC2 genes. Furthermore, we identified six variable regions as promising barcode regions. Phylogenetic analysis grouped the nine Asian taxa into six branches, with C. henryi forming the basal group from which three distinct complexes emerged. This study contributes significantly to the current understanding of the evolutionary dynamics and phylogenetic relationships within the genus Caryodaphnopsis. Furthermore, the identified molecular markers hold potential for molecular barcoding applications in population genetics, providing valuable tools for future research and conservation efforts within this diverse genus.
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Affiliation(s)
- Zhengying Cao
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yaya Qu
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, Guangxi, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China.
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China.
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Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
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Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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McLay TGB, Fowler RM, Fahey PS, Murphy DJ, Udovicic F, Cantrill DJ, Bayly MJ. Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia. Mol Phylogenet Evol 2023; 187:107869. [PMID: 37423562 DOI: 10.1016/j.ympev.2023.107869] [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: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023]
Abstract
Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.
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Affiliation(s)
- Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia.
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Patrick S Fahey
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney, Sydney 2000, NSW, Australia; Qld Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia 4072, Qld, Australia
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia
| | - David J Cantrill
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
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de Oliveira DA, da Silva PHM, Novaes E, Grattapaglia D. Genome-wide analysis highlights genetic admixture in exotic germplasm resources of Eucalyptus and unexpected ancestral genomic composition of interspecific hybrids. PLoS One 2023; 18:e0289536. [PMID: 37552668 PMCID: PMC10409294 DOI: 10.1371/journal.pone.0289536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Eucalyptus is an economically important genus comprising more than 890 species in different subgenera and sections. Approximately twenty species of subgenus Symphyomyrtus account for 95% of the world's planted eucalypts. Discrimination of closely related eucalypt taxa is challenging, consistent with their recent phylogenetic divergence and occasional hybridization in nature. Admixture, misclassification or mislabeling of Eucalyptus germplasm resources maintained as exotics have been suggested, although no reports are available. Moreover, hybrids with increased productivity and traits complementarity are planted worldwide, but little is known about their actual genomic ancestry. In this study we examined a set of 440 trees of 16 different Eucalyptus species and 44 interspecific hybrids of multi-species origin conserved in germplasm banks in Brazil. We used genome-wide SNP data to evaluate the agreement between the alleged phylogenetic classification of species and provenances as registered in their historical records, and their observed genetic clustering derived from SNP data. Genetic structure analyses correctly assigned each of the 16 species to a different cluster although the PCA positioning of E. longirostrata was inconsistent with its current taxonomy. Admixture was present for closely related species' materials derived from local germplasm banks, indicating unintended hybridization following germplasm introduction. Provenances could be discriminated for some species, indicating that SNP-based discrimination was directly proportional to geographical distance, consistent with an isolation-by-distance model. SNP-based genomic ancestry analysis showed that the majority of the hybrids displayed realized genomic composition deviating from the expected ones based on their pedigree records, consistent with admixture in their parents and pervasive genome-wide directional selection toward the fast-growing E. grandis genome. SNP data in support of tree breeding provide precise germplasm identity verification, and allow breeders to objectively recognize the actual ancestral origin of superior hybrids to more realistically guide the program toward the development of the desired genetic combinations.
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Affiliation(s)
| | | | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Dario Grattapaglia
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, Brasilia, DF, Brazil
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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Su W, Liang R. The complete chloroplast genome of a fast-growing tree Lophostemon confertus (Myrtaceae). Mitochondrial DNA B Resour 2023; 8:26-29. [PMID: 36620314 PMCID: PMC9815246 DOI: 10.1080/23802359.2022.2158691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lophostemon confertus (Myrtaceae), a fast-growing ornamental tree, is widely cultivated in tropical and subtropical regions. To determine its phylogenetic position within Myrtaceae, here we report its complete chloroplast (cp) genome, which is 160,297 bp long and contains two inverted repeats (IRs) of 26,490 bp each, separated by a small single-copy region of 18,826 bp and a large single-copy region of 88,491 bp. The cp genome contains 123 genes, including 73 unique protein-coding genes (six duplicated in the IR regions), 29 unique tRNA genes (seven duplicated in the IR regions), and four unique rRNA genes (all located in the IR regions). Phylogenetic analysis of 18 species of Myrtaceae showed that L. confertus is sister to Xanthostemon chrysanthus. The complete cp genome of L. confertus provides a valuable genetic resource for further phylogenetic studies.
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Affiliation(s)
- Wenhang Su
- Department of Art and Design, Guangxi Vocational & Technical College, Nanning, Guangxi, China
| | - Rifan Liang
- Department of Art and Design, Guangxi Vocational & Technical College, Nanning, Guangxi, China,CONTACT Rifan Liang Department of Art and DesignGuangxi, Vocational & Technical College, No. 19, Mingyang Avenue, Jiangnan District, Nanning530226, Guangxi Zhuang Autonomous Region, China
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Duan Q, Liu F, Gui D, Fan W, Cui G, Jia W, Zhu A, Wang J. Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:865606. [PMID: 35937320 PMCID: PMC9355515 DOI: 10.3389/fpls.2022.865606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/16/2022] [Indexed: 05/24/2023]
Abstract
Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but the phylogenetic relationships among wild species and their contributions to these cultivars are poorly resolved. We collected the major Lilium species and cultivars and assembled their plastome sequences. Our phylogenetic reconstruction using 114 plastid genomes, including 70 wild species representing all sections and 42 cultivars representing six hybrid divisions and two outgroups, uncovered well-supported genetic relationships within Lilium. The wild species were separated into two distinct groups (groups A and B) associated with geographical distribution, which further diversified into eight different clades that were phylogenetically well supported. Additional support was provided by the distributions of indels and single-nucleotide variants, which were consistent with the topology. The species of sections Archelirion, Sinomartagon III, and Leucolirion 6a and 6b were the maternal donors for Oriental hybrids, Asiatic hybrids, Trumpet hybrids, and Longiflorum hybrids, respectively. The maternal donors of the OT hybrids originated from the two sections Archelirion and Leucolirion 6a, and LA hybrids were derived from the two sections Leucolirion 6b and Sinomartagon. Our study provides an important basis for clarifying the infrageneric classification and the maternal origin of cultivars in Lilium.
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Affiliation(s)
- Qing Duan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfen Cui
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Wenjie Jia
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
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10
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Chen Q, Hu H, Zhang D. DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:764255. [PMID: 35283910 PMCID: PMC8914171 DOI: 10.3389/fpls.2022.764255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.
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Affiliation(s)
- Qi Chen
- College of Pharmacy, Dali University, Dali, China
| | - Haisu Hu
- College of Pharmacy, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- *Correspondence: Dequan Zhang,
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11
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Wu L, Wu M, Cui N, Xiang L, Li Y, Li X, Chen S. Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria. Chin Med 2021; 16:52. [PMID: 34225754 PMCID: PMC8256587 DOI: 10.1186/s13020-021-00460-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/26/2021] [Indexed: 12/21/2022] Open
Abstract
Background Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species. Methods We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species. Results The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level. Conclusions This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00460-z.
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Affiliation(s)
- Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingli Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ning Cui
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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12
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Simmonds SE, Smith JF, Davidson C, Buerki S. Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae). Mol Phylogenet Evol 2021; 163:107229. [PMID: 34129936 DOI: 10.1016/j.ympev.2021.107229] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152-161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.
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Affiliation(s)
- Sara E Simmonds
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | - James F Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | | | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA.
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13
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Huang X, Tan W, Li F, Liao R, Guo Z, Shi T, Gao Z. The chloroplast genome of Prunus zhengheensis: Genome comparative and phylogenetic relationships analysis. Gene 2021; 793:145751. [PMID: 34062257 DOI: 10.1016/j.gene.2021.145751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
Prunus zhengheensis is a novel species originated in Fujian province, China. However, there is no further information available on its classification and molecular biology study. In this study, we first report the complete chloroplast (cp) genome sequence of P. zhengheensis. The cp genome of P. zhengheensis is 158,106 bp and GC content is 36.73%, is a circular structure composed of LSC (large single copy), SSC (small single copy), and IR (inverted repeat) regions, with the size of the three regions being 86,321 bp, 18,999 bp and 26,393 bp, respectively. The cp genome of P. zhengheensis contains 130 genes, and 242 SSRs are identified in the cp genome. The comparative analysis of cp genomes in eight Prunus plants demonstrates the subtle divergences occur in the protein-coding gene rps18, rps12, psbF, rpl33, matK, and rbcL, and that the KA/KS nucleotide substitution ratio of the ndhF of P. zhengheensis and P. armeniaca is 1.79636. The phylogenetic results indicate that the P. zhengheensis is closely related to P. mume, compared to other species of Prunus. Our research results provide the important genomic information for molecular phylogeny of P. zhengheensis.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Li
- Jilin Academy of Agricultural Sciences, Jilin 136100, China.
| | - Ruyu Liao
- Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
| | - Zhongren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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14
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Rutherford S, Wan JSH, Cohen JM, Benson D, Rossetto M. Looks can be deceiving: speciation dynamics of co-distributed Angophora (Myrtaceae) species in a varying landscape. Evolution 2020; 75:310-329. [PMID: 33325041 DOI: 10.1111/evo.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome-wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome-wide analyses of related species in a diverse landscape can provide insights into speciation.
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Affiliation(s)
- Susan Rutherford
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Justin S H Wan
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Joel M Cohen
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Doug Benson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
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15
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Mostert-O'Neill MM, Reynolds SM, Acosta JJ, Lee DJ, Borevitz JO, Myburg AA. Genomic evidence of introgression and adaptation in a model subtropical tree species, Eucalyptus grandis. Mol Ecol 2020; 30:625-638. [PMID: 32881106 DOI: 10.1111/mec.15615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 11/27/2022]
Abstract
The genetic consequences of adaptation to changing environments can be deciphered using population genomics, which may help predict species' responses to global climate change. Towards this, we used genome-wide SNP marker analysis to determine population structure and patterns of genetic differentiation in terms of neutral and adaptive genetic variation in the natural range of Eucalyptus grandis, a widely cultivated subtropical and temperate species, serving as genomic reference for the genus. We analysed introgression patterns at subchromosomal resolution using a modified ancestry mapping approach and identified provenances with extensive interspecific introgression in response to increased aridity. Furthermore, we describe potentially adaptive genetic variation as explained by environment-associated SNP markers, which also led to the discovery of what is likely a large structural variant. Finally, we show that genes linked to these markers are enriched for biotic and abiotic stress responses.
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Affiliation(s)
- Marja Mirjam Mostert-O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sharon Melissa Reynolds
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Juan Jose Acosta
- Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - David John Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, Australia
| | - Justin O Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT, Australia
| | - Alexander Andrew Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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16
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Machado LDO, Vieira LDN, Stefenon VM, Faoro H, Pedrosa FDO, Guerra MP, Nodari RO. Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene. Genet Mol Biol 2020; 43:e20180377. [PMID: 32555941 PMCID: PMC7288672 DOI: 10.1590/1678-4685-gmb-2018-0377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/24/2019] [Indexed: 11/30/2022] Open
Abstract
Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing ‘hotspots’ of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as ‘hotspots’ of variability, and (iii) the genes identified as ‘hotspots’ of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.
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Affiliation(s)
- Lilian de Oliveira Machado
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil
| | | | - Valdir Marcos Stefenon
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil.,Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, RS, Brazil
| | - Helisson Faoro
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Curitiba, PR, Brazil
| | | | - Miguel Pedro Guerra
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil
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17
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Liu F, Movahedi A, Yang W, Xu L, Xie J, Zhang Y. The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br. Mol Biol Rep 2020; 47:5013-5024. [PMID: 32515001 DOI: 10.1007/s11033-020-05567-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022]
Abstract
Callistemon rigidus R.Br. one of the traditional Chinese medicinal plants, is acrid-flavored and mild-natured, with the prominent effects reducing swelling, resolving phlegm, and dispelling rheumatism. Clinically, it has been commonly used to treat cold, cough and asthma, pain and swelling from impact injuries, eczema, rheumatic arthralgia. The chloroplast genome study on Callistemon rigidus R.Br. is a few seen. This study demonstrates the data collected from the assembly and annotation of the chloroplast (cp) genome of Callistemon rigidus R.Br., followed by furthers comparative analysis with the cp genomes of closely related species. C. rigidus R.Br. showed a cp genome in the size of 158, 961 bp long with 36.78% GC content, among which a pair of inverted repeats (IRs) of 26, 671 bp separated a large single-copy (LSC) region of 87, 162 bp and a small single-copy (SSC) region of 18, 457 bp. Altogether 131 genes were hosted, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. 284 simple sequence repeats (SSRs) were also marked out. A comparative analysis of the genome structure and the sequence data of closely related species unveiled the conserved gene order in the IR and LSC/SSC regions, a quite constructive finding for future phylogenetic research. Overall, this study providing C. rigidus R.Br. genomic resources could positively contribute to the evolutionary study and the phylogenetic reconstruction of Myrtaceae.
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Affiliation(s)
- Fenxiang Liu
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Wenguo Yang
- Department of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Lei Xu
- Genepioneer Biotechnologies Inc., Nanjing, 210023, China
| | - Jigang Xie
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
| | - Yu Zhang
- School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China
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18
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Xie DF, Tan JB, Yu Y, Gui LJ, Su DM, Zhou SD, He XJ. Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences. ANNALS OF BOTANY 2020; 125:1039-1055. [PMID: 32239179 PMCID: PMC7262478 DOI: 10.1093/aob/mcaa024] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/01/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. METHODS In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. RESULTS Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. CONCLUSIONS Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Jin-Bo Tan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Lin-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
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19
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Yu J, Xu T, Wang H, Chen D, Dong H. The complete chloroplast genome sequence of Anogeissus acuminata (combretaceae). Mitochondrial DNA B Resour 2020; 5:2032-2033. [PMID: 33457731 PMCID: PMC7782036 DOI: 10.1080/23802359.2020.1756958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Anogeissus acuminata (Roxburgh ex Candolle) Guillemin et al. is an Endangered and dominant species of deciduous forests distributed in the Mekong valley of southwest China and adjacent Indo-China Peninsula. Here we assembled and annotated the complete chloroplast (cp) genome. It is 159,993 bp in length and encodes 84 protein-coding genes, 37 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. This chloroplast genome sequencing offers genetic background for conservation and phylogenetic studies.
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Affiliation(s)
- Jiaojun Yu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China.,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
| | - Tongmei Xu
- Pu'er Forestry and Grassland Bureau, Pu'er, China
| | - Hongyu Wang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
| | - Dange Chen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China.,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
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20
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Zheng G, Wei L, Ma L, Wu Z, Gu C, Chen K. Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships. PLANT MOLECULAR BIOLOGY 2020; 102:659-676. [PMID: 31997112 DOI: 10.1007/s11103-020-00972-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/20/2020] [Indexed: 05/11/2023]
Abstract
Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.
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Affiliation(s)
- Gang Zheng
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Lingling Wei
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- School of Humanities and social sciences, Beijing Forestry University, Beijing, 100083, China
| | - Li Ma
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Zhiqiang Wu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China.
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Kai Chen
- School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
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21
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Chen Q, Wu X, Zhang D. Comparison of the abilities of universal, super, and specific DNA barcodes to discriminate among the original species of Fritillariae cirrhosae bulbus and its adulterants. PLoS One 2020; 15:e0229181. [PMID: 32053689 PMCID: PMC7018091 DOI: 10.1371/journal.pone.0229181] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/02/2020] [Indexed: 11/18/2022] Open
Abstract
Fritillariae cirrhosae bulbus is a famous type of traditional Chinese medicine used for cough relief and eliminating phlegm. The medicine originates from dried bulbs of five species and one variety of Fritillaria. Recently, immature bulbs from other congeneric species, such as F. ussuriensis, have been sold as adulterants of Fritillariae cirrhosae bulbus in medicine markets owing to the high price and limited availability of the genuine medicine. However, it is difficult to accurately identify the bulbs from different original species of Fritillariae cirrhosae bulbus and its adulterants based on traditional methods, although such medicines have different prices and treatment efficacies. The present study adopted DNA barcoding to identify these different species and compared the discriminatory power of super, universal, and specific barcodes in Fritillaria. The results revealed that the super-barcode had strong discriminatory power (87.5%). Among universal barcodes, matK provided the best species resolution (87.5%), followed by ITS (62.5%), rbcL (62.5%), and trnH-psbA (25%). The combination of these four universal barcodes provided the highest discriminatory power (87.5%), which was equivalent to that of the super-barcode. Two plastid genes, ycf1 and psbM-psbD, had much better discriminatory power (both 87.5%) than did other plastid barcodes, and were suggested as potential specific barcodes for identifying Fritillaria species. Phylogenetic analyses indicated that F. cirrhosa was not a "good" species that was composed of multiple lineages, which might have affected the evaluation of the discriminatory ability. This study revealed that the complete plastid genome, as super barcode, was an efficient and reliable tool for identifying the original species of Fritillariae cirrhosae bulbus and its adulterants.
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Affiliation(s)
- Qi Chen
- College of Pharmacy and Chemistry, Dali University, Dali, China
| | - Xiaobo Wu
- College of Pharmacy and Chemistry, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy and Chemistry, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, China
- * E-mail:
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22
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Marsh KJ, Wallis IR, Kulheim C, Clark R, Nicolle D, Foley WJ, Salminen J. New approaches to tannin analysis of leaves can be used to explain in vitro biological activities associated with herbivore defence. THE NEW PHYTOLOGIST 2020; 225:488-498. [PMID: 31412143 PMCID: PMC6916633 DOI: 10.1111/nph.16117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/08/2023]
Abstract
Although tannins have been an important focus of studies of plant-animal interactions, traditional tannin analyses cannot differentiate between the diversity of structures present in plants. This has limited our understanding of how different mixtures of these widespread secondary metabolites contribute to variation in biological activity. We used UPLC-MS/MS to determine the concentration and broad composition of tannins and polyphenols in 628 eucalypt (Eucalyptus, Corymbia and Angophora) samples, and related these to three in vitro functional measures believed to influence herbivore defence: protein precipitation capacity, oxidative activity at high pH and capacity to reduce in vitro nitrogen (N) digestibility. Protein precipitation capacity was most strongly correlated with concentrations of procyanidin subunits in proanthocyanidins (PAs), and late-eluting ellagitannins. Capacity to reduce in vitro N digestibility was affected most by the subunit composition and mean degree of polymerisation (mDP) of PAs. Finally, concentrations of ellagitannins and prodelphinidin subunits of PAs were the strongest determinants of oxidative activity. The results illustrate why measures of total tannins rarely correlate with animal feeding responses. However, they also confirm that the analytical techniques utilised here could allow researchers to understand how variation in tannins influence the ecology of individuals and populations of herbivores, and, ultimately, other ecosystem processes.
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Affiliation(s)
- Karen J. Marsh
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Ian R. Wallis
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Carsten Kulheim
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Robert Clark
- Research School of FinanceActuarial Studies and StatisticsThe Australian National UniversityCanberraACT2601Australia
| | - Dean Nicolle
- Currency Creek ArboretumPO Box 808Melrose ParkSA5039Australia
| | - William J. Foley
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Juha‐Pekka Salminen
- Natural Chemistry Research GroupDepartment of ChemistryUniversity of TurkuTurkuFI‐20500Finland
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23
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Zhong Q, Yang S, Sun X, Wang L, Li Y. The complete chloroplast genome of the Jerusalem artichoke ( Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene. PeerJ 2019; 7:e7596. [PMID: 31531272 PMCID: PMC6718157 DOI: 10.7717/peerj.7596] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.
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Affiliation(s)
- Qiwen Zhong
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China.,Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Shipeng Yang
- Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Xuemei Sun
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China.,Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Lihui Wang
- Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Yi Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China
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24
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Chen Q, Wu X, Zhang D. Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. PeerJ 2019; 7:e7480. [PMID: 31497389 PMCID: PMC6708372 DOI: 10.7717/peerj.7480] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/15/2019] [Indexed: 01/23/2023] Open
Abstract
Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
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Affiliation(s)
- Qi Chen
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China
| | - Xiaobo Wu
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China.,Institute of Materia Medica, Dali University, Dali, Yunnan, China
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25
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Identifying genetic markers for a range of phylogenetic utility-From species to family level. PLoS One 2019; 14:e0218995. [PMID: 31369563 PMCID: PMC6675087 DOI: 10.1371/journal.pone.0218995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/13/2019] [Indexed: 12/03/2022] Open
Abstract
Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
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26
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Aspinwall MJ, Pfautsch S, Tjoelker MG, Vårhammar A, Possell M, Drake JE, Reich PB, Tissue DT, Atkin OK, Rymer PD, Dennison S, Van Sluyter SC. Range size and growth temperature influence Eucalyptus species responses to an experimental heatwave. GLOBAL CHANGE BIOLOGY 2019; 25:1665-1684. [PMID: 30746837 DOI: 10.1111/gcb.14590] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/03/2019] [Accepted: 02/04/2019] [Indexed: 05/24/2023]
Abstract
Understanding forest tree responses to climate warming and heatwaves is important for predicting changes in tree species diversity, forest C uptake, and vegetation-climate interactions. Yet, tree species differences in heatwave tolerance and their plasticity to growth temperature remain poorly understood. In this study, populations of four Eucalyptus species, two with large range sizes and two with comparatively small range sizes, were grown under two temperature treatments (cool and warm) before being exposed to an equivalent experimental heatwave. We tested whether the species with large and small range sizes differed in heatwave tolerance, and whether trees grown under warmer temperatures were more tolerant of heatwave conditions than trees grown under cooler temperatures. Visible heatwave damage was more common and severe in the species with small rather than large range sizes. In general, species that showed less tissue damage maintained higher stomatal conductance, lower leaf temperatures, larger increases in isoprene emissions, and less photosynthetic inhibition than species that showed more damage. Species exhibiting more severe visible damage had larger increases in heat shock proteins (HSPs) and respiratory thermotolerance (Tmax ). Thus, across species, increases in HSPs and Tmax were positively correlated, but inversely related to increases in isoprene emissions. Integration of leaf gas-exchange, isoprene emissions, proteomics, and respiratory thermotolerance measurements provided new insight into mechanisms underlying variability in tree species heatwave tolerance. Importantly, warm-grown seedlings were, surprisingly, more susceptible to heatwave damage than cool-grown seedlings, which could be associated with reduced enzyme concentrations in leaves. We conclude that species with restricted range sizes, along with trees growing under climate warming, may be more vulnerable to heatwaves of the future.
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Affiliation(s)
- Michael J Aspinwall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - Sebastian Pfautsch
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mark G Tjoelker
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Angelica Vårhammar
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Malcolm Possell
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - John E Drake
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Forest and Natural Resources Management, SUNY-ESF, Syracuse, New York
| | - Peter B Reich
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Department of Forest Resources, University of Minnesota, Minnesota
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Owen K Atkin
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Siobhan Dennison
- Department of Biological Science, Macquarie University, North Ryde, NSW, Australia
| | - Steven C Van Sluyter
- Department of Biological Science, Macquarie University, North Ryde, NSW, Australia
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27
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Alwadani KG, Janes JK, Andrew RL. Chloroplast genome analysis of box-ironbark Eucalyptus. Mol Phylogenet Evol 2019; 136:76-86. [PMID: 30954587 DOI: 10.1016/j.ympev.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022]
Abstract
Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
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Affiliation(s)
- Khawla G Alwadani
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science, Jazan University, Saudi Arabia
| | - Jasmine K Janes
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science and Technology, Vancouver Island University, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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28
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Pinard D, Myburg AA, Mizrachi E. The plastid and mitochondrial genomes of Eucalyptus grandis. BMC Genomics 2019; 20:132. [PMID: 30760198 PMCID: PMC6373115 DOI: 10.1186/s12864-019-5444-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/10/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes. RESULTS In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis. CONCLUSIONS The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.
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Affiliation(s)
- Desre Pinard
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
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29
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Wang W, Schalamun M, Morales-Suarez A, Kainer D, Schwessinger B, Lanfear R. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics 2018; 19:977. [PMID: 30594129 PMCID: PMC6311037 DOI: 10.1186/s12864-018-5348-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Chloroplasts are organelles that conduct photosynthesis in plant and algal cells. The information chloroplast genome contained is widely used in agriculture and studies of evolution and ecology. Correctly assembling chloroplast genomes can be challenging because the chloroplast genome contains a pair of long inverted repeats (10-30 kb). Typically, it is simply assumed that the gross structure of the chloroplast genome matches the most commonly observed structure of two single-copy regions separated by a pair of inverted repeats. The advent of long-read sequencing technologies should remove the need to make this assumption by providing sufficient information to completely span the inverted repeat regions. Yet, long-reads tend to have higher error rates than short-reads, and relatively little is known about the best way to combine long- and short-reads to obtain the most accurate chloroplast genome assemblies. Using Eucalyptus pauciflora, the snow gum, as a test case, we evaluated the effect of multiple parameters, such as different coverage of long-(Oxford nanopore) and short-(Illumina) reads, different long-read lengths, different assembly pipelines, with a view to determining the most accurate and efficient approach to chloroplast genome assembly. RESULTS Hybrid assemblies combining at least 20x coverage of both long-reads and short-reads generated a single contig spanning the entire chloroplast genome with few or no detectable errors. Short-read-only assemblies generated three contigs (the long single copy, short single copy and inverted repeat regions) of the chloroplast genome. These contigs contained few single-base errors but tended to exclude several bases at the beginning or end of each contig. Long-read-only assemblies tended to create multiple contigs with a much higher single-base error rate. The chloroplast genome of Eucalyptus pauciflora is 159,942 bp, contains 131 genes of known function. CONCLUSIONS Our results suggest that very accurate assemblies of chloroplast genomes can be achieved using a combination of at least 20x coverage of long- and short-reads respectively, provided that the long-reads contain at least ~5x coverage of reads longer than the inverted repeat region. We show that further increases in coverage give little or no improvement in accuracy, and that hybrid assemblies are more accurate than long-read-only or short-read-only assemblies.
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Affiliation(s)
- Weiwen Wang
- Research School of Biology, Australian National University, Canberra, Australia.
| | - Miriam Schalamun
- Research School of Biology, Australian National University, Canberra, Australia.,Institute of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - David Kainer
- Research School of Biology, Australian National University, Canberra, Australia
| | | | - Robert Lanfear
- Research School of Biology, Australian National University, Canberra, Australia
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30
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Vilasboa J, Da Costa CT, Fett-Neto AG. Rooting of eucalypt cuttings as a problem-solving oriented model in plant biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:85-97. [PMID: 30557533 DOI: 10.1016/j.pbiomolbio.2018.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 02/07/2023]
Abstract
Species of Eucalyptus are some of the most planted trees in the world, providing fiber, cellulose, energy, and wood for construction and furniture in renewable fashion, with the added advantage of fixing large amounts of atmospheric carbon. The efficiency of eucalypts in forestry relies mostly on the clonal propagation of selected genotypes both as pure species and interspecific hybrids. The formation of new roots from cambium tissues at the base of cuttings, referred to as adventitious rooting (AR), is essential for accomplishing clonal propagation successfully. AR is a highly complex, multi-level regulated developmental process, affected by a number of endogenous and environmental factors. In several cases, highly desirable genotypes from an industrial point of view carry along the undesirable trait of difficulty-to-root (recalcitrance). Understanding the bases of this phenotype is needed to identify ways to overcome recalcitrance and allow efficient clonal propagation. Herein, an overview of the state-of-the-art on the basis of AR recalcitrance in eucalypts addressed at various levels of regulation (transcript, protein, metabolite and phenotype), and OMICs techniques is presented. In addition, a focus is also provided on the gaps that need to be filled in order to advance in this strategic biological problem for global forestry industry relying on eucalypts.
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Affiliation(s)
- Johnatan Vilasboa
- Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), P.O. Box 15005, Porto Alegre, RS, 91501-970, Brazil
| | - Cibele Tesser Da Costa
- Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), P.O. Box 15005, Porto Alegre, RS, 91501-970, Brazil
| | - Arthur Germano Fett-Neto
- Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), P.O. Box 15005, Porto Alegre, RS, 91501-970, Brazil.
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31
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Schuster TM, Setaro SD, Tibbits JFG, Batty EL, Fowler RM, McLay TGB, Wilcox S, Ades PK, Bayly MJ. Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae). PLoS One 2018; 13:e0195034. [PMID: 29668710 PMCID: PMC5905893 DOI: 10.1371/journal.pone.0195034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/15/2018] [Indexed: 11/19/2022] Open
Abstract
Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9-10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes.
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Affiliation(s)
- Tanja M. Schuster
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, Birdwood Avenue, South Yarra, VIC, Australia
- * E-mail:
| | - Sabrina D. Setaro
- Department of Biology, Wake Forest University, Winston-Salem, NC,United States of America
| | - Josquin F. G. Tibbits
- Department of Economic Development, Jobs, Transport and Resources, AgriBiosciences Centre, La Trobe University, Bundoora, VIC, Australia
| | - Erin L. Batty
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Rachael M. Fowler
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Todd G. B. McLay
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Stephen Wilcox
- Genomics Hub, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, Australia
| | - Peter K. Ades
- School of Ecosystem and Forest Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
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Sampson J, Tapper S, Coates D, Hankinson M, Mcarthur S, Byrne M. Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jane Sampson
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Sarah Tapper
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - David Coates
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Maggie Hankinson
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Shelley Mcarthur
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
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Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Sci Rep 2018; 8:1184. [PMID: 29352182 PMCID: PMC5775360 DOI: 10.1038/s41598-018-19591-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People’s Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.
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Röschenbleck J, Wicke S, Weinl S, Kudla J, Müller KF. Genus-Wide Screening Reveals Four Distinct Types of Structural Plastid Genome Organization in Pelargonium (Geraniaceae). Genome Biol Evol 2018; 9:64-76. [PMID: 28172771 PMCID: PMC5381562 DOI: 10.1093/gbe/evw271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
Geraniaceae are known for their unusual plastid genomes (plastomes), with the genus Pelargonium being most conspicuous with regard to plastome size and gene organization as judged by the sequenced plastomes of P. x hortorum and P. alternans. However, the hybrid origin of P. x hortorum and the uncertain phylogenetic position of P. alternans obscure the events that led to these extraordinary plastomes. Here, we examine all plastid reconfiguration hotspots for 60 Pelargonium species across all subgenera using a PCR and sequencing approach. Our reconstruction of the rearrangement history revealed four distinct plastome types. The ancestral plastome configuration in the two subgenera Magnipetala and Pelargonium is consistent with that of the P. alternans plastome, whereas that of the subgenus Parvulipetala deviates from this organization by one synapomorphic inversion in the trnNGUU–ndhF region. The plastome of P. x hortorum resembles those of one group of the subgenus Paucisignata, but differs from a second group by another inversion in the psaI–psaJ region. The number of microstructural changes and amount of repetitive DNA are generally elevated in all inverted regions. Nucleotide substitution rates correlate positively with the number of indels in all regions across the different subgenera. We also observed lineage- and species-specific changes in the gene content, including gene duplications and fragmentations. For example, the plastid rbcL–psaI region of Pelargonium contains a highly variable accD-like region. Our results suggest alternative evolutionary paths under possibly changing modes of plastid transmission and indicate the non-functionalization of the plastid accD gene in Pelargonium.
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Affiliation(s)
- Joachim Röschenbleck
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
- Institute for Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
- Corresponding author: E-mail:
| | - Stefan Weinl
- Institute for Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Jörg Kudla
- Institute for Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Kai F. Müller
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
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Marsh KJ, Kulheim C, Blomberg SP, Thornhill AH, Miller JT, Wallis IR, Nicolle D, Salminen JP, Foley WJ. Genus-wide variation in foliar polyphenolics in eucalypts. PHYTOCHEMISTRY 2017; 144:197-207. [PMID: 28957714 DOI: 10.1016/j.phytochem.2017.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 05/11/2023]
Abstract
Many studies quantify total phenolics or total tannins, but understanding the ecological role of polyphenolic secondary metabolites requires at least an understanding of the diversity of phenolic groups present. We used UPLC-MS/MS to measure concentrations of different polyphenol groups - including the four most common tannin groups, the three most common flavonoid groups, and quinic acid derivatives - in foliage from 628 eucalypts from the genera Eucalyptus, Angophora and Corymbia. We also tested for phylogenetic signal in each of the phenolic groups. Many eucalypts contained high concentrations of polyphenols, particularly ellagitannins, which have been relatively poorly studied, but may possess strong oxidative activity. Because the biosynthetic pathways of many phenolic compounds share either precursors or enzymes, we found negative correlations between the concentrations of several of the constituents that we measured, including proanthocyanidins (PAs) and hydrolysable tannins (HTs), HTs and flavonol derivatives, and HTs and quinic acid derivatives. We observed moderate phylogenetic signal in all polyphenol constituents, apart from the concentration of the prodelphinidin subunit of PAs and the mean degree of polymerisation of PAs. These two traits, which have previously been shown to be important in determining plants' protein precipitation capacity, may have evolved under selection, perhaps in response to climate or herbivore pressure. Hence, the signature of evolutionary history appears to have been erased for these traits. This study is an important step in moving away from analysing "totals" to a better understanding of how phylogenetic effects influence phenolic composition, and how this in turn influences ecological processes.
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Affiliation(s)
- Karen J Marsh
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Carsten Kulheim
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon P Blomberg
- School of Biological Sciences, University of Queensland, St Lucia, 4072, Australia
| | - Andrew H Thornhill
- Centre for Australian National Biodiversity Research, CSIRO National Research Collections, GPO Box 1600, Canberra, ACT, 2601, Australia; Australian Tropical Herbarium, James Cook University, Cairns, QLD, 4870, Australia
| | - Joseph T Miller
- Centre for Australian National Biodiversity Research, CSIRO National Research Collections, GPO Box 1600, Canberra, ACT, 2601, Australia; Office of International Science and Engineering, National Science Foundation, Arlington, VA, 22230, USA
| | - Ian R Wallis
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Dean Nicolle
- Currency Creek Arboretum, PO Box 808, Melrose Park, SA, 5039, Australia
| | - Juha-Pekka Salminen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20500, Turku, Finland
| | - William J Foley
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Eguiluz M, Yuyama PM, Guzman F, Rodrigues NF, Margis R. Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora. Genet Mol Biol 2017; 40:871-876. [PMID: 29111566 PMCID: PMC5738614 DOI: 10.1590/1678-4685-gmb-2017-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/13/2017] [Indexed: 12/02/2022] Open
Abstract
Plinia trunciflora is a Brazilian native fruit tree from the
Myrtaceae family, also known as jaboticaba. This species has great potential by
its fruit production. Due to the high content of essential oils in their leaves
and of anthocyanins in the fruits, there is also an increasing interest by the
pharmaceutical industry. Nevertheless, there are few studies focusing on its
molecular biology and genetic characterization. We herein report the complete
chloroplast (cp) genome of P. trunciflora using high-throughput
sequencing and compare it to other previously sequenced Myrtaceae genomes. The
cp genome of P. trunciflora is 159,512 bp in size, comprising
inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and
18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding,
30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding
genes demonstrated that P. trunciflora, Eugenia uniflora and
Acca sellowiana form a cluster with closer relationship to
Syzygium cumini than with Eucalyptus. The
complete cp sequence reported here can be used in evolutionary and population
genetics studies, contributing to resolve the complex taxonomy of this species
and fill the gap in genetic characterization.
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Affiliation(s)
- Maria Eguiluz
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Priscila Mary Yuyama
- Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Frank Guzman
- Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Nureyev Ferreira Rodrigues
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Biofísica, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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37
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Du YP, Bi Y, Yang FP, Zhang MF, Chen XQ, Xue J, Zhang XH. Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses. Sci Rep 2017; 7:5751. [PMID: 28720853 PMCID: PMC5515919 DOI: 10.1038/s41598-017-06210-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/08/2017] [Indexed: 12/19/2022] Open
Abstract
Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses. The genomes ranged from 151,655 bp to 153,235 bp in length and had a typical quadripartite structure with a conserved genome arrangement and moderate divergence. A comparison of sixteen Lilium chloroplast genomes revealed ten mutation hotspots. Single nucleotide polymorphisms (SNPs) for any two Lilium chloroplast genomes ranged from 8 to 1,178 and provided robust data for phylogeny. Except for some of the shortest internodes, phylogenetic relationships of the Lilium species inferred from the chloroplast genome obtained high support, indicating that chloroplast genome data will be useful to help resolve the deeper branches of phylogeny.
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Affiliation(s)
- Yun-Peng Du
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yu Bi
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- School of Horticulture, Jilin Agricultural University, Changchun, Jilin Province, 130000, China
| | - Feng-Ping Yang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ming-Fang Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xu-Qing Chen
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jing Xue
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiu-Hai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Wu Z, Gu C, Tembrock LR, Zhang D, Ge S. Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species. PLoS One 2017; 12:e0177553. [PMID: 28542519 PMCID: PMC5443529 DOI: 10.1371/journal.pone.0177553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B). A total of 110 unique genes are annotated, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. The genome structure, gene order, GC content, and other features are similar to those of other angiosperm cp genomes. When comparing the cp genomes between Oryzinae and Zizaniinae subtribes, the main differences were found between the junction regions and distribution of simple sequence repeats (SSRs). In comparing the two Chikusichloa species, the genomes were only 40 bp different in length and 108 polymorphic sites, including 83 single nucleotide substitutions (SNPs) and 25 insertion-deletions (Indels), were found between the whole cp genomes. The complete cp genome of C. mutica will be an important genetic tool for future breeding programs and understanding the evolution of wild rice relatives.
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Affiliation(s)
- Zhiqiang Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Dong Zhang
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Bui EN, Thornhill AH, González-Orozco CE, Knerr N, Miller JT. Climate and geochemistry as drivers of eucalypt diversification in Australia. GEOBIOLOGY 2017; 15:427-440. [PMID: 28371135 DOI: 10.1111/gbi.12235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/27/2017] [Indexed: 06/07/2023]
Abstract
Eucalypts cover most of Australia. Here, we investigate the relative contribution of climate and geochemistry to the distribution and diversity of eucalypts. Using geostatistics, we estimate major element concentrations, pH, and electrical conductivity at sites where eucalypts have been recorded. We compare the median predicted geochemistry and reported substrate for individual species that appear associated with extreme conditions; this provides a partial evaluation of the predictions. We generate a site-by-species matrix by aggregating observations to the centroids of 100-km-wide grid cells, calculate diversity indices, and use numerical ecology methods (ordination, variation partitioning) to investigate the ecology of eucalypts and their response to climatic and geochemical gradients. We find that β-diversity coincides with variations in climatic and geochemical patterns. Climate and geochemistry together account for less than half of the variation in eucalypt species assemblages across Australia but for greater than 80% in areas of high species richness. Climate is more important than geochemistry in explaining eucalypts species distribution and change in assemblages across Australia as a whole but there are correlations between the two sets of environmental variables. Many individual eucalypt species and entire taxonomic sections (Aromatica, Longistylus of subgenus Eucalyptus, Dumaria, and Liberivalvae of subgenus Symphyomyrtus) have distributions affected strongly by geochemistry. We conclude that eucalypt diversity is driven by steep geochemical gradients that have arisen as climate patterns have fluctuated over Australia over the Cenozoic, generally aridifying since the Miocene. The diversification of eucalypts across Australia is thus an excellent example of co-evolution of landscapes and biota in space and time and challenges accepted notions of macroecology.
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Affiliation(s)
- E N Bui
- CSIRO Land and Water, Canberra, ACT, Australia
| | - A H Thornhill
- Centre for Australian National Biodiversity Research, CSIRO Plant Industry, Canberra, ACT, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, Qld, Australia
| | - C E González-Orozco
- Centre for Australian National Biodiversity Research, CSIRO Plant Industry, Canberra, ACT, Australia
| | - N Knerr
- Centre for Australian National Biodiversity Research, CSIRO Plant Industry, Canberra, ACT, Australia
| | - J T Miller
- Centre for Australian National Biodiversity Research, CSIRO Plant Industry, Canberra, ACT, Australia
- Office of International Science and Engineering, National Science Foundation, Arlington, VA, USA
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40
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Flores-Rentería L, Rymer PD, Riegler M. Unpacking boxes: Integration of molecular, morphological and ecological approaches reveals extensive patterns of reticulate evolution in box eucalypts. Mol Phylogenet Evol 2017; 108:70-87. [DOI: 10.1016/j.ympev.2017.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/26/2022]
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41
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Phylogenomic relationship of feijoa (Acca sellowiana (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences. Genetica 2017; 145:163-174. [DOI: 10.1007/s10709-017-9954-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/19/2017] [Indexed: 10/20/2022]
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42
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High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus. Mol Phylogenet Evol 2016; 105:63-85. [DOI: 10.1016/j.ympev.2016.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/29/2016] [Accepted: 08/12/2016] [Indexed: 01/07/2023]
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43
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Reginato M, Neubig KM, Majure LC, Michelangeli FA. The first complete plastid genomes of Melastomataceae are highly structurally conserved. PeerJ 2016; 4:e2715. [PMID: 27917315 PMCID: PMC5131623 DOI: 10.7717/peerj.2715] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 11/20/2022] Open
Abstract
Background In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. Methods Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information. Results The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of rps16 and rpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%. Discussion Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.
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Affiliation(s)
- Marcelo Reginato
- Institute of Systematic Botany, The New York Botanical Garden , Bronx, New York , United States
| | - Kurt M Neubig
- Department of Plant Biology, Southern Illinois University of Carbondale , Carbondale, Illinois , United States
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden , Phoenix, Arizona , United States
| | - Fabian A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden , Bronx, New York , United States
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44
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Jo S, Kim HW, Kim YK, Cheon SH, Kim KJ. Complete plastome sequence of Psidium guajava L. (Myrtaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:612-614. [PMID: 33490414 PMCID: PMC7800272 DOI: 10.1080/23802359.2016.1209096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this study, we determined the complete plastome sequence of Psidium guajava L. (Myrtaceae) (NCBI acc. no. KX364403). The gene order and structure of the P. guajava plastome are similar to those of a typical angiosperm. The complete plastome is 158,841 bp in length, and consists of a large single copy of 87,675 bp and a small single copy of 18,464 bp, separated by two inverted repeats of 26,351 bp. The overall AT content of the sequence is 63.0%. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 100 simple sequence loci were identified from the genome. Phylogenetic analysis revealed that P. guajava is a sister group of Eugenia uniflora with 100% bootstrap support.
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Affiliation(s)
- Sangjin Jo
- School of Life Sciences, Korea University, Seoul, Korea
| | - Hoe-Won Kim
- School of Life Sciences, Korea University, Seoul, Korea
| | - Young-Kee Kim
- School of Life Sciences, Korea University, Seoul, Korea
| | - Se-Hwan Cheon
- School of Life Sciences, Korea University, Seoul, Korea
| | - Ki-Joong Kim
- School of Life Sciences, Korea University, Seoul, Korea
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 756] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Bardon L, Sothers C, Prance GT, Malé PJG, Xi Z, Davis CC, Murienne J, García-Villacorta R, Coissac E, Lavergne S, Chave J. Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes. AMERICAN JOURNAL OF BOTANY 2016; 103:1089-1102. [PMID: 27329943 DOI: 10.3732/ajb.1500463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 05/04/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear. METHODS We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family. KEY RESULTS The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification. CONCLUSIONS Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.
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Affiliation(s)
- Léa Bardon
- Laboratoire Evolution et Diversité Biologique UMR 5174 CNRS, ENFA, Université Paul Sabatier 31062 Toulouse, France
| | - Cynthia Sothers
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Ghillean T Prance
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Pierre-Jean G Malé
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Jerome Murienne
- Laboratoire Evolution et Diversité Biologique UMR 5174 CNRS, ENFA, Université Paul Sabatier 31062 Toulouse, France
| | | | - Eric Coissac
- Université Grenoble Alpes, CNRS, UMR 5553 LECA, F-38000 Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, CNRS, UMR 5553 LECA, F-38000 Grenoble, France
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique UMR 5174 CNRS, ENFA, Université Paul Sabatier 31062 Toulouse, France
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Turner B, Paun O, Munzinger J, Chase MW, Samuel R. Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence. ANNALS OF BOTANY 2016; 117:1175-85. [PMID: 27098088 PMCID: PMC4904177 DOI: 10.1093/aob/mcw060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/10/2016] [Accepted: 02/26/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely related Diospyros species. METHODS Twenty-two closely related Diospyros species from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices. KEY RESULTS The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New Caledonian Diospyros species. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species. CONCLUSIONS In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New Caledonian Diospyros species, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree because the total number of variable sites was much lower than in the entire plastid genome. The geographical clustering of the individuals against a background of overall low sequence divergence could indicate transfer of plastid genomes due to hybridization and introgression following secondary contact.
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Affiliation(s)
- Barbara Turner
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Wien, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Wien, Austria
| | | | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Wien, Austria
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Gu C, Tembrock LR, Johnson NG, Simmons MP, Wu Z. The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae). PLoS One 2016; 11:e0150752. [PMID: 26950701 PMCID: PMC4780714 DOI: 10.1371/journal.pone.0150752] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/17/2016] [Indexed: 11/19/2022] Open
Abstract
Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of Lagerstroemia fauriei. To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of L. fauriei and several other Lythraceae species lack the rpl2 intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of L. fauriei provides a much needed genetic resource for further phylogenetic research in Lagerstroemia and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications.
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Affiliation(s)
- Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, P.R. China
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Nels G. Johnson
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, 37996, Tennessee, United States of America
| | - Mark P. Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
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Williams AV, Miller JT, Small I, Nevill PG, Boykin LM. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia. Mol Phylogenet Evol 2016; 96:1-8. [DOI: 10.1016/j.ympev.2015.11.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
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Gardner AG, Sessa EB, Michener P, Johnson E, Shepherd KA, Howarth DG, Jabaily RS. Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies. Mol Phylogenet Evol 2015; 94:605-617. [PMID: 26463342 DOI: 10.1016/j.ympev.2015.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/18/2015] [Accepted: 10/02/2015] [Indexed: 12/25/2022]
Abstract
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
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Affiliation(s)
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA
| | - Pryce Michener
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Eden Johnson
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Parks and Wildlife, Kensington, WA 6151, Australia
| | - Dianella G Howarth
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
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