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Li H, Wang L, Ma C. The complete plastome of Campsis radicans (L.) Bureau 1864 and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1200-1204. [PMID: 38239913 PMCID: PMC10796121 DOI: 10.1080/23802359.2023.2275827] [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: 06/21/2023] [Accepted: 10/21/2023] [Indexed: 01/22/2024] Open
Abstract
Campsis radicans (L.) Bureau 1864, a species of Bignoniaceae, has a widespread paleotropical distribution and is utilized for horticultural and traditional Chinese medicinal purposes. Despite the plant's significance, its genetic diversity must be better understood. In this study, we have successfully assembled and characterized the complete plastome of C. radicans, marking a significant advancement toward comprehending its genetic composition. The plastome is 153,630 bp long and harbors 130 genes, including 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Our phylogenomic analysis of the representative species of Bignoniaceae indicated that C. radicans formed a monophyletic sister clade of Campsis with C. grandiflora. These findings are crucial for conserving and utilizing this important plant species. They also highlight the potential for future research into the evolution and preservation of C. radicans, which could be advantageous in pharmaceutical applications.
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Affiliation(s)
- Hongqin Li
- College of Pharmacy, Heze University, Heze, P. R. China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, P. R. China
| | - Changhao Ma
- Inspection Department Three, Shandong Center for Food and Drug Evaluation and Inspection, Jinan, P. R. China
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2
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Yan R, Geng Y, Jia Y, Xiang C, Zhou X, Hu G. Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1265641. [PMID: 37828930 PMCID: PMC10565954 DOI: 10.3389/fpls.2023.1265641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
Introduction The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
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Affiliation(s)
- Rongrong Yan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yanfei Geng
- College of Tea Science, Guizhou University, Guiyang, Guizhou, China
| | - Yuhuan Jia
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Chunlei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xinxin Zhou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoxiong Hu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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3
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Fonseca LHM, Carlsen MM, Fine PVA, Lohmann LG. A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae. Front Genet 2023; 13:1085692. [PMID: 36699458 PMCID: PMC9869424 DOI: 10.3389/fgene.2022.1085692] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The plant family Bignoniaceae is a conspicuous and charismatic element of the tropical flora. The family has a complex taxonomic history, with substantial changes in the classification of the group during the past two centuries. Recent re-classifications at the tribal and generic levels have been largely possible by the availability of molecular phylogenies reconstructed using Sanger sequencing data. However, our complete understanding of the systematics, evolution, and biogeography of the family remains incomplete, especially due to the low resolution and support of different portions of the Bignoniaceae phylogeny. To overcome these limitations and increase the amount of molecular data available for phylogeny reconstruction within this plant family, we developed a bait kit targeting 762 nuclear genes, including 329 genes selected specifically for the Bignoniaceae; 348 genes obtained from the Angiosperms353 with baits designed specifically for the family; and, 85 low-copy genes of known function. On average, 77.4% of the reads mapped to the targets, and 755 genes were obtained per species. After removing genes with putative paralogs, 677 loci were used for phylogenetic analyses. On-target genes were compared and combined in the Exon-Only dataset, and on-target + off-target regions were combined in the Supercontig dataset. We tested the performance of the bait kit at different taxonomic levels, from family to species-level, using 38 specimens of 36 different species of Bignoniaceae, representing: 1) six (out of eight) tribal level-clades (e.g., Bignonieae, Oroxyleae, Tabebuia Alliance, Paleotropical Clade, Tecomeae, and Jacarandeae), only Tourrettieae and Catalpeae were not sampled; 2) all 20 genera of Bignonieae; 3) seven (out of nine) species of Dolichandra (e.g., D. chodatii, D. cynanchoides, D. dentata, D. hispida, D. quadrivalvis, D. uncata, and D. uniguis-cati), only D. steyermarkii and D. unguiculata were not sampled; and 4) three individuals of Dolichandra unguis-cati. Our data reconstructed a well-supported phylogeny of the Bignoniaceae at different taxonomic scales, opening new perspectives for a comprehensive phylogenetic framework for the family as a whole.
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Affiliation(s)
- Luiz Henrique M. Fonseca
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil,Systematic and Evolutionary Botany Laboratory, Department of Biology, Ghent University, Ghent, Belgium,*Correspondence: Luiz Henrique M. Fonseca, ; Lúcia G. Lohmann,
| | | | - Paul V. A. Fine
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Lúcia G. Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil,University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States,*Correspondence: Luiz Henrique M. Fonseca, ; Lúcia G. Lohmann,
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4
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Fonseca LHM, Nazareno AG, Thode VA, Zuntini AR, Lohmann LG. Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine. PeerJ 2022; 10:e13207. [PMID: 35415013 PMCID: PMC8995027 DOI: 10.7717/peerj.13207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/10/2022] [Indexed: 01/12/2023] Open
Abstract
The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.
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Affiliation(s)
- Luiz Henrique M. Fonseca
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Department of Biology, Ghent University, Ghent, Flanders, Belgium
| | - Alison G. Nazareno
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Verônica A. Thode
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Alexandre R. Zuntini
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Royal Botanic Gardens, Kew, London, United Kingdom
| | - Lúcia G. Lohmann
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil
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5
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Chen H, Chen Z, Du Q, Jiang M, Wang B, Liu C. Complete chloroplast genome of Campsis grandiflora (Thunb.) schum and systematic and comparative analysis within the family Bignoniaceae. Mol Biol Rep 2022; 49:3085-3098. [DOI: 10.1007/s11033-022-07139-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/12/2022] [Indexed: 11/30/2022]
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6
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Li X, St Laurent R, Earl C, Doorenweerd C, van Nieukerken EJ, Davis DR, Johns CA, Kawakita A, Kobayashi S, Zwick A, Lopez-Vaamonde C, Ohshima I, Kawahara AY. Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data. Cladistics 2021; 38:277-300. [PMID: 34710244 DOI: 10.1111/cla.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/27/2022] Open
Abstract
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.
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Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Services, University of Hawaii, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | | | - Donald R Davis
- Department of Entomology, NHB 105, Smithsonian Institution, Washington, DC, USA
| | - Chris A Johns
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Kawakita
- The Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, 112-0001, Japan
| | - Shigeki Kobayashi
- Entomological Laboratory, Graduate School of life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Andreas Zwick
- Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orléans, France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
| | - Issei Ohshima
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan.,Center for Frontier Natural History, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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7
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Combining molecular and geographical data to infer the phylogeny of Lamiales and its dispersal patterns in and out of the tropics. Mol Phylogenet Evol 2021; 164:107287. [PMID: 34365014 DOI: 10.1016/j.ympev.2021.107287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
Lamiales is one of the most intractable orders of flowering plants, with several changes in family composition, and circumscription throughout history. The order is worldwide distributed, occurring in tropical forests and frozen habitats. In this study, a comprehensive phylogeny of Lamiales was reconstructed using DNA sequences. The tree was used to infer dispersal patterns, focusing on the tropics and extratropics. Molecular and species geographic data available from public repositories were combined to address both objectives. A total of 6,910 species, and 842 genera of Lamiales were sampled using the Python tool PyPHLAWD. The tree was inferred using RAxML, and recovered a monophyletic Lamiales. All 26 families were recovered as monophyletic with high support. The families Bignoniaceae, and Plantaginaceae are remarkable examples. The first emerged as monophyletic and included tribe Jacarandeae, while the later emerged as monophyletic in its sensu lato and included both the tribes Angelonieae, and Gratioleae. Distribution points for all species were retrieved from GBIF. After filtering, 1,136,425 records were retained. Species were coded as present in extratropical or tropical environments. The in and out of the tropics dispersal patterns were inferred using a maximum likelihood approach that identifies hidden rate changes. The model recovered higher rates of transition from extratropics to tropics, estimating two rates of state transitions. When ancestral states are considered, more discrete transitions from extratropics to tropics were observed. The extratropical state was also inferred for the crown node of Lamiales and old nested nodes, revealing a rare pattern of transitions to the tropics throughout the upper Cretaceous and Tertiary. A significant phylogenetic signal was recovered for the in and out of the tropics dispersal patterns, showing that state transitions are not frequent enough to erase the effect of tree structure on the data.
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8
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Lima DF, Goldenberg R, Forest F, Cowan RS, Lucas EJ. Phylogeny and biogeography of Myrcia sect. Aguava (Myrtaceae, Myrteae) based on phylogenomic and Sanger data provide evidence for a Cerrado origin and geographically structured clades. Mol Phylogenet Evol 2020; 157:107043. [PMID: 33346112 DOI: 10.1016/j.ympev.2020.107043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/18/2022]
Abstract
Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed.
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Affiliation(s)
- Duane F Lima
- Programa de Pós-Graduação em Biologia Vegetal, IB, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil.
| | - Renato Goldenberg
- Departamento de Botânica, SCB, Universidade Federal do Paraná, 81531-970 Curitiba, PR, Brazil
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Robyn S Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Eve J Lucas
- Herbarium, Royal Botanic Gardens, Kew, TW9 3AB Richmond, Surrey, United Kingdom
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9
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Sobreiro MB, Vieira LD, Nunes R, Novaes E, Coissac E, Silva-Junior OB, Grattapaglia D, Collevatti RG. Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae. PLANTA 2020; 252:91. [PMID: 33098500 DOI: 10.1007/s00425-020-03498-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.
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Affiliation(s)
- Mariane B Sobreiro
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Lucas D Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Evandro Novaes
- Laboratório de Genética Molecular, Departamento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200-900, Brazil
| | - Eric Coissac
- Laboratoire d'Écologie Alpine (LECA), University Grenoble-Alpes, Grenoble, Switzerland
| | | | - Dario Grattapaglia
- EMBRAPA Recursos Genéticos e Biotecnologia, EPqB, Brasília, DF, 70770-910, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.
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10
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Fonseca LHM, Lohmann LG. Characterization of the first chloroplast genome of Tabebuia (Bignoniaceae). Mitochondrial DNA B Resour 2020; 5:2954-2956. [PMID: 33458015 PMCID: PMC7782154 DOI: 10.1080/23802359.2020.1791003] [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: 06/08/2020] [Accepted: 06/20/2020] [Indexed: 11/05/2022] Open
Abstract
The chloroplast genome of Tabebuia nodosa is described and characterized here. This species is endemic to the Chaco and the first species of Tabebuia to have its organelle genome sequenced, providing a genomic resource for phylogenetic inferences. The plastome of T. nodosa is 158,454 bp in length, with a large single-copy of 85,406 bp, a small single-copy of 12,785 bp, and inverted repeats of 30,116 bp each. It contains 131 genes, with 86 protein-coding genes, 37 tRNA, and 8 rRNA. Overall, the GC content is 38.2%. The T. nodosa plastome resembles the structural organization of plastomes commonly found in flowering plants, including those of other genera of Bignoniaceae. A phylogenetic analysis combining a subset of Bignoniaceae plastomes confirms the placement of T. nodosa within the Tabebuia alliance with maximum support.
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Affiliation(s)
- Luiz Henrique M. Fonseca
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lúcia G. Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Ji Y, Yang L, Chase MW, Liu C, Yang Z, Yang J, Yang JB, Yi TS. Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae). BMC PLANT BIOLOGY 2019; 19:543. [PMID: 31805856 PMCID: PMC6896732 DOI: 10.1186/s12870-019-2147-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/19/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. RESULTS All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. CONCLUSIONS Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Lifang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Mark W. Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS UK
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
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Zhou Y, Zhang YQ, Xing XC, Zhang JQ, Ren Y. Straight From the Plastome: Molecular Phylogeny and Morphological Evolution of Fargesia (Bambusoideae: Poaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:981. [PMID: 31447865 PMCID: PMC6691181 DOI: 10.3389/fpls.2019.00981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/11/2019] [Indexed: 06/04/2023]
Abstract
Fargesia is ecologically and economically important in mountainous forests. Many Fargesia species are also important sources of food for some endangered animals such as the giant panda. Recent molecular phylogenetic analyses have revealed Fargesia as a polyphyletic group despite some unclear lineage affinities. In the present study, we reconstructed the phylogeny of Fargesia and its allies, including Thamnocalamus, Arundinaria (incl. Bashania), Yushania, Indocalamus, Ampelocalamus and Phyllostachys, from a plastome sequence matrix that contained 20 Fargesia and five Yushania species as ingroups, 16 species from nine other bamboo genera plus Oryza sativa and Zea mays as outgroups. Fargesia and its allies were broken into eight clades. Several Fargesia species were clustered into the Thamnocalamus clade and the Drepanostachyum + Himalayacalamus clade that rendered the polyphyly of Fargesia. The remaining six clades, including the Fargesia spathe clade, the Phyllostachys clade, Arundinaria fargesii, the Ampelocalamus clade, the Fargesia grossa clade, and the Fargesia macclureana clade, were identified. Molecular phylogenetic analyses supported that Yushania should be included in Fargesia (s.l.) which had synapomorphy of expanded leaf sheaths in varying degree at the basis of inflorescences, and further divided into the Fargesia spathe clade, the Fargesia grossa clade, and the Fargesia macclureana clade. All sampled species of Yushania were nested within the Fargesia grossa clade. The probable model of the origin of the species in the Fargesia spathe clade with spathe-like leaf sheath syndrome was proposed. Moreover, the formation of the spathe-like leaf sheath syndrome may be correlated with cold climatic conditions in Quaternary. Our results provide new sight into the phylogenetic relationship within Fargesia.
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Affiliation(s)
| | | | | | - Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Yi Ren
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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Herrando-Moraira S. Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae). Mol Phylogenet Evol 2018; 128:69-87. [PMID: 30036700 DOI: 10.1016/j.ympev.2018.07.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain.
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