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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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Pouchon C, Boluda CG. REFMAKER: make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae. Mol Phylogenet Evol 2023:107826. [PMID: 37257798 DOI: 10.1016/j.ympev.2023.107826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10% of the produced libraries, and the low coverage associated with these libraries (< 3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can next be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.
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Affiliation(s)
- Charles Pouchon
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland.
| | - Carlos G Boluda
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland
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Jiao B, Chen C, Wei M, Niu G, Zheng J, Zhang G, Shen J, Vitales D, Vallès J, Verloove F, Erst AS, Soejima A, Mehregan I, Kokubugata G, Chung GY, Ge X, Gao L, Yuan Y, Joly C, Jabbour F, Wang W, Shultz LM, Gao T. Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy. ANNALS OF BOTANY 2023; 131:867-883. [PMID: 36976653 PMCID: PMC10184459 DOI: 10.1093/aob/mcad051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/24/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance and ecological significance, a well-resolved phylogeny for global Artemisia, a natural generic delimitation and infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling and insufficient information on DNA markers. Its morphological characters, such as capitulum, life form and leaf, show marked variations and are widely used in its infrageneric taxonomy. However, their evolution within Artemisia is poorly understood. Here, we aimed to reconstruct a well-resolved phylogeny for global Artemisia via a phylogenomic approach, to infer the evolutionary patterns of its key morphological characters and to update its circumscription and infrageneric taxonomy. METHODS We sampled 228 species (258 samples) of Artemisia and its allies from both fresh and herbarium collections, covering all the subgenera and its main geographical areas, and conducted a phylogenomic analysis based on nuclear single nucleotide polymorphisms (SNPs) obtained from genome skimming data. Based on the phylogenetic framework, we inferred the possible evolutionary patterns of six key morphological characters widely used in its previous taxonomy. KEY RESULTS The genus Kaschgaria was revealed to be nested in Artemisia with strong support. A well-resolved phylogeny of Artemisia consisting of eight highly supported clades was recovered, two of which were identified for the first time. Most of the previously recognized subgenera were not supported as monophyletic. Evolutionary inferences based on the six morphological characters showed that different states of these characters originated independently more than once. CONCLUSIONS The circumscription of Artemisia is enlarged to include the genus Kaschgaria. The morphological characters traditionally used for the infrageneric taxonomy of Artemisia do not match the new phylogenetic tree. They experienced a more complex evolutionary history than previously thought. We propose a revised infrageneric taxonomy of the newly circumscribed Artemisia, with eight recognized subgenera to accommodate the new results.
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Affiliation(s)
- Bohan Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohao Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiye Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guojin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahao Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada al CSIC, Facultat de Farmàcia i Ciències de l'Alimentació -Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain
| | - Filip Verloove
- Meise Botanic Garden, Nieuwelaan 38, B-1860 Meise, Belgium
| | - Andrey S Erst
- Laboratory Herbarium (NS), Central Siberian Botanical Garden, Russian Academy of Sciences Russia, Novosibirsk, 630090, Zolotodolinskaya st. 101, Russia
- Tomsk State University, Laboratoryof Systematics and Phylogeny of Plants (TK), Tomsk 634050, Russia
| | - Akiko Soejima
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Iraj Mehregan
- Laboratory for Plant Molecular Phylogeny and Systematics, Department of Biology, Science and Research Branch, Azad University, Tehran, Iran
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan
| | - Gyu-Young Chung
- Department of Forest Science, Andong National University, 1375 Gyeongdong-ro Andong, Gyeongsangbuk-do, 36729, Republic of Korea
| | - Xuejun Ge
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lianming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Lijiang National Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan 67410, China
| | - Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Cyprien Joly
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier CP39, 75005 Paris, France
| | - Florian Jabbour
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier CP39, 75005 Paris, France
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leila M Shultz
- Department of Wildland Resources, Utah State University, Logan, UT 84322-5230, USA
| | - Tiangang Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Garrett N, Viruel J, Klimpert N, Soto Gomez M, Lam VKY, Merckx VSFT, Graham SW. Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales). AMERICAN JOURNAL OF BOTANY 2023; 110:e16141. [PMID: 36779918 DOI: 10.1002/ajb2.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome. METHODS We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω). RESULTS Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK. CONCLUSIONS We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.
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Affiliation(s)
- Natalie Garrett
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Nathaniel Klimpert
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1098, XH, Amsterdam, The Netherlands
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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Ji Y, Landis JB, Yang J, Wang S, Zhou N, Luo Y, Liu H. Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics. ANNALS OF BOTANY 2023; 131:301-312. [PMID: 36434782 PMCID: PMC9992941 DOI: 10.1093/aob/mcac144] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Asparagaceae subfamily Nolinoideae is an economically important plant group, but the deep relationships and evolutionary history of the lineage remain poorly understood. Based on a large data set including 37 newly sequenced samples and publicly available plastomes, this study aims to better resolve the inter-tribal relationships of Nolinoideae, and to rigorously examine the tribe-level monophyly of Convallarieae, Ophiopogoneae and Polygonateae. METHODS Maximum likelihood (ML) and Bayesian inference (BI) methods were used to infer phylogenetic relationships of Nolinoideae at the genus level and above. The diversification history of Nolinoideae was explored using molecular dating. KEY RESULTS Both ML and BI analyses identically recovered five clades within Nolinoideae, respectively corresponding to Dracaeneae + Rusceae, Polygonateae + Theropogon, Ophiopogoneae, Nolineae, and Convallarieae excluding Theropogon, and most deep nodes were well supported. As Theropogon was embedded in Polygonateae, the plastome phylogeny failed to resolve Convallarieae and Polygonateae as reciprocally monophyletic. Divergence time estimation showed that the origins of most Nolinoideae genera were dated to the Miocene and Pliocene. The youthfulness of Nolinoideae genera is well represented in the three herbaceous tribes (Convallarieae, Ophiopogoneae and Polygonateae) chiefly distributed in temperate areas of the Northern Hemisphere, as the median stem ages of all 14 genera currently belonging to them were estimated at <12.37 Ma. CONCLUSIONS This study recovered a robust backbone phylogeny, providing new insights for better understanding the evolution and classification of Nolinoideae. Compared with the deep relationships recovered by a previous study based on transcriptomic data, our data suggest that ancient hybridization or incomplete lineage sorting may have occurred in the early diversification of Nolinoideae. Our findings will provide important reference for further study of the evolutionary complexity of Nolinoideae using nuclear genomic data. The recent origin of these herbaceous genera currently belonging to Convallarieae, Ophiopogoneae and Polygonateae provides new evidence to support the hypothesis that the global expansion of temperate habitats caused by the climate cooling over the past 15 million years may have dramatically driven lineage diversification and speciation in the Northern Hemisphere temperate flora.
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Affiliation(s)
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Nian Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Luo
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Lin Q, Braukmann TWA, Soto Gomez M, Mayer JLS, Pinheiro F, Merckx VSFT, Stefanović S, Graham SW. Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny. THE NEW PHYTOLOGIST 2022; 236:1908-1921. [PMID: 35731179 DOI: 10.1111/nph.18335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/13/2022] [Indexed: 05/03/2023]
Abstract
Fully mycoheterotrophic plants can be difficult to place in plant phylogeny due to elevated substitution rates associated with photosynthesis loss. This potentially limits the effectiveness of downstream analyses of mycoheterotrophy that depend on accurate phylogenetic inference. Although mitochondrial genomic data sets are rarely used in plant phylogenetics, theory predicts that they should be resilient to long-branch artefacts, thanks to their generally slow evolution, coupled with limited rate elevation in heterotrophs. We examined the utility of mitochondrial genomes for resolving contentious higher-order placements of mycoheterotrophic lineages in two test cases: monocots (focusing on Dioscoreales) and Ericaceae. We find Thismiaceae to be distantly related to Burmanniaceae in the monocot order Dioscoreales, conflicting with current classification schemes based on few gene data sets. We confirm that the unusual Afrothismia is related to Taccaceae-Thismiaceae, with a corresponding independent loss of photosynthesis. In Ericaceae we recovered the first well supported relationships among its five major lineages: mycoheterotrophic Ericaceae are not monophyletic, as pyroloids are inferred to be sister to core Ericaceae, and monotropoids to arbutoids. Genes recovered from mitochondrial genomes collectively resolved previously ambiguous mycoheterotroph higher-order relationships. We propose that mitochondrial genomic data should be considered in standardised gene panels for inferring overall plant phylogeny.
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Affiliation(s)
- Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Thomas W A Braukmann
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. FRONTIERS IN PLANT SCIENCE 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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Volis S, Zhang Y, Deng T, Yusupov Z. Dark-colored Oncocyclus irises in Israel analyzed by AFLP, whole chloroplast genome sequencing and species distribution modeling. Isr J Ecol Evol 2022. [DOI: 10.1163/22244662-bja10037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The Haynei is one of seven species aggregates (clusters of species having similar flower morphology) recognized in section Oncocyclus of genus Iris. This aggregate, characterized by dark-colored flowers, is represented by six species in Israel and adjacent Jordan. There is, however, no knowledge of the genetic relationship of these species making verification of their taxonomic status impossible. We investigated genetic variation in this group using analysis of whole chloroplast genomes and amplified fragment length polymorphism (AFLP). We also used species distribution modeling (SDM) to predict species ranges under current climatic conditions. We found some population groups within the currently recognized species of section Oncocyclus to represent dramatically different genetic entities which devaluates a general trend of merging many previously recognized species of section Oncocyclus based on their flower morphology. Despite the importance of homoploid hybridization in this group’s evolution and some apparently sporadically happening inter-specific gene flow, the main evolutionary forces in Oncocyclus appear to be vicariance and spatial isolation. Our findings suggest that some of the currently recognized species in section Oncocyclus need revision. A revision must be based on genetic analyses allowing the reconstruction of ancestry and recognition of the importance of vicariance and spatial isolation in the evolution of this group. The implications of the present findings for conservation are discussed.
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Affiliation(s)
- Sergei Volis
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Yonghong Zhang
- Life Science Department, Yunnan Normal University, Kunming, 650204, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Ziyoviddin Yusupov
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
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9
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Coyotee Howard C, Crowl AA, Harvey TS, Cellinese N. Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae). Mol Phylogenet Evol 2022; 169:107430. [DOI: 10.1016/j.ympev.2022.107430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
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10
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Yu Y, Han Y, Peng Y, Tian Z, Zeng P, Zong H, Zhou T, Cai J. Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae. Chin Med 2021; 16:125. [PMID: 34823565 PMCID: PMC8620154 DOI: 10.1186/s13020-021-00538-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. METHODS In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. RESULTS The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. CONCLUSIONS Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.
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Affiliation(s)
- Yang Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Yuwei Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Peng Zeng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078 Macau, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Tinggan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
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11
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Arias T, Niederhuth CE, McSteen P, Pires JC. The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype. FRONTIERS IN PLANT SCIENCE 2021; 12:637115. [PMID: 33747016 PMCID: PMC7973465 DOI: 10.3389/fpls.2021.637115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.
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12
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Namgung J, Do HDK, Kim C, Choi HJ, Kim JH. Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae). Sci Rep 2021; 11:3262. [PMID: 33547390 PMCID: PMC7865063 DOI: 10.1038/s41598-021-82692-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.
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Affiliation(s)
- Ju Namgung
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea
| | - Hoang Dang Khoa Do
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea
- Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Changkyun Kim
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Gyeongsangnamdo, 51140, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea.
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13
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Yoo MJ, Lee BY, Kim S, Lim CE. Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:645735. [PMID: 34305959 PMCID: PMC8296909 DOI: 10.3389/fpls.2021.645735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/16/2021] [Indexed: 05/14/2023]
Abstract
The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, NY, United States
| | - Byoung-Yoon Lee
- National Institute of Biological Resources, Incheon, South Korea
| | - Sangtae Kim
- Department of Biotechnology, Sungshin Women’s University, Seoul, South Korea
| | - Chae Eun Lim
- National Institute of Biological Resources, Incheon, South Korea
- *Correspondence: Chae Eun Lim,
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14
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Hall ND, Zhang H, Mower JP, McElroy JS, Goertzen LR. The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content within Poaceae. Genome Biol Evol 2020; 12:3684-3697. [PMID: 31665327 PMCID: PMC7145533 DOI: 10.1093/gbe/evz229] [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] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Plant mitochondrial (mt) genome assembly provides baseline data on size, structure, and gene content, but resolving the sequence of these large and complex organelle genomes remains challenging due to fragmentation, frequent recombination, and transfers of DNA from neighboring plastids. The mt genome for Eleusine indica (Poaceae: goosegrass) is comprehensibly analyzed here, providing key reference data for an economically significant invasive species that is also the maternal parent of the allotetraploid crop Finger millet (Eleusine coracana). The assembled E. indica genome contains 33 protein coding genes, 6 rRNA subunits, 24 tRNA, 8 large repetitive regions 15 kb of transposable elements across a total of 520,691 bp. Evidence of RNA editing and loss of rpl2, rpl5, rps14, rps11, sdh4, and sdh3 genes is evaluated in the context of an updated survey of mt genomic gene content across the grasses through an analysis of publicly available data. Hypothesized patterns of Poaceae mt gene loss are examined in a phylogenetic context to clarify timing, showing that rpl2 was transferred to the nucleus from the mitochondrion prior to the origin of the PACMAD clade.
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Affiliation(s)
- Nathan D Hall
- Department of Biological Sciences, Auburn University
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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15
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Soto Gomez M, Lin Q, Silva Leal E, Gallaher TJ, Scherberich D, Mennes CB, Smith SY, Graham SW. A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns. Cladistics 2020; 36:481-504. [DOI: 10.1111/cla.12417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marybel Soto Gomez
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Qianshi Lin
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Eduardo Silva Leal
- Universidade Federal Rural da Amazônia, Campus Capanema Avenida Barão de Capanema s/n Capanema68700-665 PA Brazil
| | | | - David Scherberich
- Jardin Botanique de la Ville de Lyon Mairie de Lyon69205 Lyon Cedex 01 France
| | | | - Selena Y. Smith
- Department of Earth & Environmental Sciences and Museum of Paleontology University of Michigan Ann Arbor MI 48109 USA
| | - Sean W. Graham
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
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16
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Gunn BF, Murphy DJ, Walsh NG, Conran JG, Pires JC, Macfarlane TD, Birch JL. Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia. Mol Phylogenet Evol 2020; 149:106836. [PMID: 32304826 DOI: 10.1016/j.ympev.2020.106836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 02/03/2023]
Abstract
Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia and possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy that are potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inference criteria, based on plastome data from genome-skimming to infer relationships. A fossil-calibrated chronogram provided a temporal framework for understanding trait transitions. Ancestral state reconstructions and phylogenetic comparative trait correlation analyses provided insights into the evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca. 56.61 million years ago (95% highest posterior density values 70.31-45.34 million years) and the major lineages diversified since the Oligocene. The most recent common ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. Biome occupancy transitions were correlated with polyploidy and the presence of storage roots. Polyploidy potentially serves as an "enabler" trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.
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Affiliation(s)
- Bee F Gunn
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
| | - Neville G Walsh
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
| | - John G Conran
- The University of Adelaide, School of Biological Sciences, Adelaide, SA 5005, Australia.
| | - J Chris Pires
- University of Missouri, Div. of Biological Sciences, 105 Tucker Hall, Columbia, MO 65211-7400, USA.
| | - Terry D Macfarlane
- Dept. of Biodiversity, Conservation and Attractions, 17 Dick Perry Ave., Technology Park, Western Precinct, Kensington, WA 6983, Australia.
| | - Joanne L Birch
- The University of Melbourne, School of BioSciences, Parkville, VIC 3010, Australia.
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17
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Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Pușcaș M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM, Coissac E. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material. PLANTS (BASEL, SWITZERLAND) 2020; 9:E432. [PMID: 32244605 PMCID: PMC7238428 DOI: 10.3390/plants9040432] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Sebastien Lavergne
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | - Marti Boleda
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - Youri Lammers
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Charles Pouchon
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Iva Pitelkova
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Mihai Pușcaș
- A. Borza Botanical Garden and Faculty of Biology and Geology, Babeș-Bolyai University, 400015 Cluj-Napoca, Romania;
| | - Cristina Roquet
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193 Bellaterra, Spain
| | - Bogdan-Iuliu Hurdu
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania;
| | - Wilfried Thuiller
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | | | - Eric Coissac
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
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Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae). Mol Phylogenet Evol 2020; 145:106729. [DOI: 10.1016/j.ympev.2019.106729] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 01/02/2023]
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19
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Munyao JN, Dong X, Yang JX, Mbandi EM, Wanga VO, Oulo MA, Saina JK, Musili PM, Hu GW. Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E296. [PMID: 32121524 PMCID: PMC7154914 DOI: 10.3390/plants9030296] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022]
Abstract
The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.
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Affiliation(s)
- Jacinta N. Munyao
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Dong
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Elijah M. Mbandi
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Vincent O. Wanga
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Millicent A. Oulo
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Josphat K. Saina
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Paul M. Musili
- East Africa Herbarium, National Museums of Kenya, P.O. Box 45166 00100 Nairobi, Kenya;
| | - Guang-Wan Hu
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Malakasi P, Bellot S, Dee R, Grace OM. Museomics Clarifies the Classification of Aloidendron (Asphodelaceae), the Iconic African Tree Aloes. FRONTIERS IN PLANT SCIENCE 2019; 10:1227. [PMID: 31681358 PMCID: PMC6803536 DOI: 10.3389/fpls.2019.01227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 05/24/2023]
Abstract
Arborescent succulent plants are regarded as keystone and indicator species in desert ecosystems due to their large stature and long lifespans. Tree aloes, the genus Aloidendron, are icons of the southern African deserts yet have proved elusive subjects due to the difficulty of obtaining material of known provenance for comparative study. Consequently, evolutionary relationships among representatives of the unusual arborescent life form have remained unclear until now. We used a museomics approach to overcome this challenge. Chloroplast genomes of six Aloidendron species and 12 other members of Asphodelaceae were sequenced from modern living collections and herbarium specimens, including the type specimens of all but two Aloidendron species, the earliest of which was collected 130 years ago. Maximum-likelihood trees estimated from full chloroplast genomes and the nuclear internal transcribed spacer (ITS) region show that Aloidendron sabaeum, from the Arabian Peninsula, is nested within Aloe while the Madagascar endemic Aloestrela suzannae is most closely related to the Somalian Aloidendron eminens. We observed phylogenetic conflicts between the plastid and nuclear topologies, which may be indicative of recurrent hybridisation or incomplete lineage sorting events in Aloe and in Aloidendron. Comparing species ecology in the context provided by our phylogeny suggests that habitat preference to either xeric deserts or humid forests/thickets evolved repeatedly in Aloidendron. Our findings demonstrate the value of botanical collections for the study and classification of taxonomically challenging succulent plants.
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Li SF, Li JR, Wang J, Dong R, Jia KL, Zhu HW, Li N, Yuan JH, Deng CL, Gao WJ. Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution. BMC PLANT BIOLOGY 2019; 19:361. [PMID: 31419941 PMCID: PMC6698032 DOI: 10.1186/s12870-019-1975-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. RESULTS A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. CONCLUSIONS These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ke-Li Jia
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
- SanQuan Medical College, Xinxiang Medical University, Xinxiang, 453003 China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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Xie DF, Yu HX, Price M, Xie C, Deng YQ, Chen JP, Yu Y, Zhou SD, He XJ. Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome. FRONTIERS IN PLANT SCIENCE 2019; 10:460. [PMID: 31114591 PMCID: PMC6503222 DOI: 10.3389/fpls.2019.00460] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
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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, China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuan Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi-Qi Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Pfanzelt S, Albach DC, von Hagen KB. Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales). PeerJ 2019; 7:e6244. [PMID: 30671303 PMCID: PMC6339776 DOI: 10.7717/peerj.6244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/08/2018] [Indexed: 12/01/2022] Open
Abstract
Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
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Affiliation(s)
- Simon Pfanzelt
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben/Seeland, Saxony-Anhalt, Germany.,Institute of Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Lower Saxony, Germany
| | - Dirk C Albach
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Lower Saxony, Germany
| | - K Bernhard von Hagen
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Lower Saxony, Germany
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Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum. Mol Phylogenet Evol 2018; 129:202-213. [DOI: 10.1016/j.ympev.2018.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023]
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Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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Hodel RGJ, Knowles LL, McDaniel SF, Payton AC, Dunaway JF, Soltis PS, Soltis DE. Terrestrial species adapted to sea dispersal: Differences in propagule dispersal of two Caribbean mangroves. Mol Ecol 2018; 27:4612-4626. [DOI: 10.1111/mec.14894] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Richard G. J. Hodel
- Department of Biology; University of Florida; Gainesville Florida
- Florida Museum of Natural History; University of Florida; Gainesville Florida
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan
| | - Stuart F. McDaniel
- Department of Biology; University of Florida; Gainesville Florida
- The Genetics Institute; University of Florida; Gainesville Florida
| | - Adam C. Payton
- Department of Biology; University of Florida; Gainesville Florida
| | | | - Pamela S. Soltis
- Florida Museum of Natural History; University of Florida; Gainesville Florida
- The Genetics Institute; University of Florida; Gainesville Florida
- The Biodiversity Institute; University of Florida; Gainesville Florida
| | - Douglas E. Soltis
- Department of Biology; University of Florida; Gainesville Florida
- Florida Museum of Natural History; University of Florida; Gainesville Florida
- The Genetics Institute; University of Florida; Gainesville Florida
- The Biodiversity Institute; University of Florida; Gainesville Florida
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Filyushin MA, Mazur AM, Shchennikova AV, Kochieva ЕZ. Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is different: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.
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Manzanilla V, Kool A, Nguyen Nhat L, Nong Van H, Le Thi Thu H, de Boer HJ. Phylogenomics and barcoding of Panax: toward the identification of ginseng species. BMC Evol Biol 2018; 18:44. [PMID: 29614961 PMCID: PMC5883351 DOI: 10.1186/s12862-018-1160-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. CONCLUSIONS MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.
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Affiliation(s)
- V Manzanilla
- The Natural History Museum, University of Oslo, Oslo, Norway.
| | - A Kool
- The Natural History Museum, University of Oslo, Oslo, Norway
| | - L Nguyen Nhat
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Nong Van
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Le Thi Thu
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H J de Boer
- The Natural History Museum, University of Oslo, Oslo, Norway
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McKain MR, Johnson MG, Uribe‐Convers S, Eaton D, Yang Y. Practical considerations for plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1038. [PMID: 29732268 PMCID: PMC5895195 DOI: 10.1002/aps3.1038] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/13/2018] [Indexed: 05/10/2023]
Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project-dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-and-coming technologies that may help propel the field even further.
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Affiliation(s)
- Michael R. McKain
- Department of Biological SciencesThe University of AlabamaBox 870344TuscaloosaAlabama35487USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main Street, Box 43131LubbockTexas79409USA
| | - Simon Uribe‐Convers
- Department of Ecology and Evolutionary BiologyUniversity of Michigan830 North UniversityAnn ArborMichigan48109USA
| | - Deren Eaton
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam AvenueNew YorkNew York10027USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota–Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108USA
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Berger BA, Han J, Sessa EB, Gardner AG, Shepherd KA, Ricigliano VA, Jabaily RS, Howarth DG. The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700042. [PMID: 29109919 PMCID: PMC5664964 DOI: 10.3732/apps.1700042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/07/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. METHODS Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. RESULTS Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. DISCUSSION Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
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Affiliation(s)
- Brent A. Berger
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Jiahong Han
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, Florida 32611 USA
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, California 95382 USA
| | - Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington 6151, Western Australia, Australia
| | - Vincent A. Ricigliano
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Road, Tucson, Arizona 85719 USA
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee 38112 USA
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
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Bruun-Lund S, Clement WL, Kjellberg F, Rønsted N. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae). Mol Phylogenet Evol 2017; 109:93-104. [DOI: 10.1016/j.ympev.2016.12.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 12/22/2016] [Accepted: 12/23/2016] [Indexed: 11/26/2022]
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McKain MR, McNeal JR, Kellar PR, Eguiarte LE, Pires JC, Leebens-Mack J. Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae). AMERICAN JOURNAL OF BOTANY 2016; 103:1717-1729. [PMID: 27793858 DOI: 10.3732/ajb.1600198] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/03/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Yucca species are ideal candidates for the study of coevolution due to the obligate mutualism they form with yucca moth pollinators (genera Tegeticula and Parategeticula). Yuccas are not the only species to exhibit a mutualism with yucca moths; the genus Hesperoyucca is pollinated by the California yucca moth (Tegeticula maculata). Relationships among yuccas, Hesperoyucca, and other members of subfamily Agavoideae are necessary to understand the evolution of this unique pollination syndrome. Here, we investigate evolutionary relationships of yuccas and closely related genera looking at the timing and origin of yucca moth pollination. METHODS In this study, we sequenced the chloroplast genomes of 20 species in the subfamily Agavoideae (Asparagaceae) and three confamilial outgroup taxa to resolve intergeneric phylogenetic relationships of Agavoideae. We estimated divergence times using protein-coding genes from 67 chloroplast genomes sampled across monocots to determine the timing of the yucca moth pollination origin. KEY RESULTS We confidently resolved intergeneric relationships in Agavoideae, demonstrating the origin of the yucca-yucca moth mutualism on two distinct lineages that diverged 27 million years ago. Comparisons of Yucca and Hesperoyucca divergence time to those of yucca moths (Tegeticula and Parategeticula, Prodoxidae) indicate overlapping ages for the origin of pollinating behavior in the moths and pollination by yucca moths in the two plant lineages. CONCLUSION Whereas pollinating yucca moths have been shown to have a single origin within the Prodoxidae, there were independent acquisitions of active pollination on lineages leading to Yucca and Hesperoyucca within the Agavoideae.
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Affiliation(s)
- Michael R McKain
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri 63132 USA
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, Georgia 30602 USA
| | - Joel R McNeal
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, Georgia 30602 USA
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, 1000 Chastain Road, Kennesaw, Georgia 30144 USA
| | - P Roxanne Kellar
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182 USA
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 311 Bond Life Sciences Center, 1201 East Rollins Street, Columbia, Missouri 65211 USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, Georgia 30602 USA
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McKain MR, Hartsock RH, Wohl MM, Kellogg EA. Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. Bioinformatics 2016; 33:130-132. [PMID: 27634949 PMCID: PMC5408774 DOI: 10.1093/bioinformatics/btw583] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/30/2016] [Accepted: 09/02/2016] [Indexed: 11/14/2022] Open
Abstract
Motivation Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. Results Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. Availability and Implementation Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/. It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ryan H Hartsock
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Molly M Wohl
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Vallejo-Marín M, Cooley AM, Lee MY, Folmer M, McKain MR, Puzey JR. Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. AMERICAN JOURNAL OF BOTANY 2016; 103:1272-88. [PMID: 27221281 DOI: 10.3732/ajb.1500471] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/16/2016] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for "maternal-excess" crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins of Mimulus peregrinus, an allohexaploid recently derived from the triploid M. ×robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. METHODS We used reciprocal crosses between the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to determine the viability of triploid M. ×robertsii hybrids resulting from paternal- vs. maternal-excess crosses. To investigate whether experimental results predict patterns seen in the field, we performed parentage analyses comparing natural populations of M. peregrinus to its diploid, tetraploid, and triploid progenitors. Organellar sequences obtained from pre-existing genomic data, supplemented with additional genotyping was used to establish the maternal ancestry of multiple M. peregrinus and M. ×robertsii populations. KEY RESULTS We found strong evidence for asymmetric origins of M. peregrinus, but opposite to the common pattern, with paternal-excess crosses significantly more successful than maternal-excess crosses. These results successfully predicted hybrid formation in nature: 111 of 114 M. ×robertsii individuals, and 27 of 27 M. peregrinus, had an M. guttatus maternal haplotype. CONCLUSION This study, which includes the first Mimulus chloroplast genome assembly, demonstrates the utility of parentage analysis through genome skimming. We highlight the benefits of complementing genomic analyses with experimental approaches to understand asymmetry in allopolyploid speciation.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Science, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA UK
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington 99362 USA
| | - Michelle Yuequi Lee
- Biological and Environmental Science, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA UK
| | - Madison Folmer
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23185 USA
| | - Michael R McKain
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 USA
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23185 USA
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016; 97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
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Welker CAD, Souza-Chies TT, Longhi-Wagner HM, Peichoto MC, McKain MR, Kellogg EA. Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae-Andropogoneae): Taxonomic implications and evidence of interspecific hybridization. Mol Phylogenet Evol 2016; 99:155-167. [PMID: 26947710 DOI: 10.1016/j.ympev.2016.02.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 01/04/2023]
Abstract
Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, it is a challenging task for several reasons, including the low interspecies variability of markers currently used in phylogenetic reconstructions and the occurrence of reticulate evolution and polyploidy in many lineages of flowering plants. The first phylogeny of the grass genus Eriochrysis is presented here, focusing on the New World species, in order to examine its relationships to other genera of the subtribe Saccharinae/tribe Andropogoneae and to define the circumscriptions of its taxonomically complicated species. Molecular cloning and sequencing of five regions of four low-copy nuclear genes (apo1, d8, ep2-ex7 and ep2-ex8, kn1) were performed, as well as complete plastome sequencing. Trees were reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference analyses. The present phylogenetic analyses indicate that Eriochrysis is monophyletic and the Old World E. pallida is sister to the New World species. Subtribe Saccharinae is polyphyletic, as is the genus Eulalia. Based on nuclear and plastome sequences plus morphology, we define the circumscriptions of the New World species of Eriochrysis: E. laxa is distinct from E. warmingiana, and E. villosa is distinct from E. cayennensis. Natural hybrids occur between E. laxa and E. villosa. The hybrids are probably tetraploids, based on the number of paralogues in the nuclear gene trees. This is the first record of a polyploid taxon in the genus Eriochrysis. Some incongruities between nuclear genes and plastome analyses were detected and are potentially caused by incomplete lineage sorting and/or ancient hybridization. The set of low-copy nuclear genes used in this study seems to be sufficient to resolve phylogenetic relationships and define the circumscriptions of other species complexes in the grass family and relatives, even in the presence of polyploidy and reticulate evolution. Complete plastome sequencing is also a promising tool for phylogenetic inference.
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Affiliation(s)
- Cassiano A D Welker
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil.
| | - Tatiana T Souza-Chies
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil.
| | - Hilda M Longhi-Wagner
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil.
| | - Myriam Carolina Peichoto
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias (UNNE), Sargento Cabral 2131, Corrientes 3400, Argentina.
| | - Michael R McKain
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.
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Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, Davis JI. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. THE NEW PHYTOLOGIST 2016; 209:855-70. [PMID: 26350789 DOI: 10.1111/nph.13617] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/23/2015] [Indexed: 05/03/2023]
Abstract
Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.
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Affiliation(s)
- Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Jason R Comer
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - John G Conran
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia
| | - Sean C Lahmeyer
- Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA
| | | | - Jeff Li
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, 92521, USA
| | - Gwynne S Lim
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Dustin R Mayfield-Jones
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Leticia Perez
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Jesus Medina
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Cristian Santos
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Dennis Wm Stevenson
- Pfizer Laboratory of Molecular Systematics, New York Botanical Garden, Bronx, NY, 10458, USA
| | - Wendy B Zomlefer
- Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA
| | - Jerrold I Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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Wang Y, Zhan DF, Jia X, Mei WL, Dai HF, Chen XT, Peng SQ. Complete Chloroplast Genome Sequence of Aquilaria sinensis (Lour.) Gilg and Evolution Analysis within the Malvales Order. FRONTIERS IN PLANT SCIENCE 2016; 7:280. [PMID: 27014304 PMCID: PMC4781844 DOI: 10.3389/fpls.2016.00280] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/21/2016] [Indexed: 05/11/2023]
Abstract
Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal plant. Moreover, the results will enhance our understanding about the evolution of cp genomes of the Malvales order, particularly with regard to the role of A. sinensis in plant systematics and evolution.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Di-Feng Zhan
- College of Agronomy, Hainan UniversityHaikou, China
| | - Xian Jia
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen UniversityXiamen, China
| | - Wen-Li Mei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Hao-Fu Dai
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Xiong-Ting Chen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- *Correspondence: Xiong-Ting Chen
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- Shi-Qing Peng
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Ross TG, Barrett CF, Soto Gomez M, Lam VK, Henriquez CL, Les DH, Davis JI, Cuenca A, Petersen G, Seberg O, Thadeo M, Givnish TJ, Conran J, Stevenson DW, Graham SW. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 2015; 32:160-178. [DOI: 10.1111/cla.12133] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- T. Gregory Ross
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Craig F. Barrett
- Department of Biological Sciences 5151 State University Dr. California State University Los Angeles CA 90032‐8201 USA
| | - Marybel Soto Gomez
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Vivienne K.Y. Lam
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Claudia L. Henriquez
- Evolution, Ecology & Population Biology Division of Biology Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Donald H. Les
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269‐3043 USA
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology Cornell University Ithaca NY 14853 USA
| | - Argelia Cuenca
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | | | | | - John Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre School of Biological Sciences Benham Bldg DX 650 312 The University of Adelaide Adelaide SA 5005 Australia
| | | | - Sean W. Graham
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
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Kim HT, Kim JS, Moore MJ, Neubig KM, Williams NH, Whitten WM, Kim JH. Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries. PLoS One 2015; 10:e0142215. [PMID: 26558895 PMCID: PMC4641739 DOI: 10.1371/journal.pone.0142215] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/19/2015] [Indexed: 12/26/2022] Open
Abstract
Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
| | - Jung Sung Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
| | - Michael J. Moore
- Department of Biology, Oberlin College, Oberlin, Ohio, United States of America
| | - Kurt M. Neubig
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Norris H. Williams
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - W. Mark Whitten
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
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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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Stadermann KB, Weisshaar B, Holtgräwe D. SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome. BMC Bioinformatics 2015; 16:295. [PMID: 26377912 PMCID: PMC4573686 DOI: 10.1186/s12859-015-0726-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Third generation sequencing methods, like SMRT (Single Molecule, Real-Time) sequencing developed by Pacific Biosciences, offer much longer read length in comparison to Next Generation Sequencing (NGS) methods. Hence, they are well suited for de novo- or re-sequencing projects. Sequences generated for these purposes will not only contain reads originating from the nuclear genome, but also a significant amount of reads originating from the organelles of the target organism. These reads are usually discarded but they can also be used for an assembly of organellar replicons. The long read length supports resolution of repetitive regions and repeats within the organelles genome which might be problematic when just using short read data. Additionally, SMRT sequencing is less influenced by GC rich areas and by long stretches of the same base. RESULTS We describe a workflow for a de novo assembly of the sugar beet (Beta vulgaris ssp. vulgaris) chloroplast genome sequence only based on data originating from a SMRT sequencing dataset targeted on its nuclear genome. We show that the data obtained from such an experiment are sufficient to create a high quality assembly with a higher reliability than assemblies derived from e.g. Illumina reads only. The chloroplast genome is especially challenging for de novo assembling as it contains two large inverted repeat (IR) regions. We also describe some limitations that still apply even though long reads are used for the assembly. CONCLUSIONS SMRT sequencing reads extracted from a dataset created for nuclear genome (re)sequencing can be used to obtain a high quality de novo assembly of the chloroplast of the sequenced organism. Even with a relatively small overall coverage for the nuclear genome it is possible to collect more than enough reads to generate a high quality assembly that outperforms short read based assemblies. However, even with long reads it is not always possible to clarify the order of elements of a chloroplast genome sequence reliantly which we could demonstrate with Fosmid End Sequences (FES) generated with Sanger technology. Nevertheless, this limitation also applies to short read sequencing data but is reached in this case at a much earlier stage during finishing.
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Affiliation(s)
- Kai Bernd Stadermann
- Chair of Genome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany. .,Bioinformatics Resource Facility, Centre for Biotechnology, Bielefeld University, Bielefeld, Germany.
| | - Bernd Weisshaar
- Chair of Genome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Daniela Holtgräwe
- Chair of Genome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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Washburn JD, Schnable JC, Davidse G, Pires JC. Phylogeny and photosynthesis of the grass tribe Paniceae. AMERICAN JOURNAL OF BOTANY 2015; 102:1493-505. [PMID: 26373976 DOI: 10.3732/ajb.1500222] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/18/2015] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved. METHODS Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used to build a phylogenetic tree of the Paniceae based on 102 markers (78 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction analyses were also performed within the Paniceae using both the traditional and two subtype classification systems to test hypotheses of C4 subtype evolution. KEY RESULTS The phylogenetic tree resolves many areas of the Paniceae with high support and provides insight into the origin and number of C4 evolution events within the tribe. The recovered phylogeny and ancestral state reconstructions support between four and seven independent origins of C4 photosynthesis within the tribe and indicate which species are potentially the closest C3 sister taxa of each of these events. CONCLUSIONS Although the sequence of evolutionary events that produced multiple C4 subtypes within the Paniceae remains undetermined, the results presented here are consistent with only a subset of currently proposed models. The species used in this study constitute a panel of C3 and C4 grasses that are suitable for further studies on C4 photosynthesis, bioenergy, food and forage crops, and various developmental features of the Paniceae.
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Affiliation(s)
- Jacob D Washburn
- Division of Biological Sciences, University of Missouri, 311 Bond Life Sciences Center, Columbia, Missouri 65211 USA
| | - James C Schnable
- Agronomy & Horticulture, University of Nebraska-Lincoln, Beadle Center E207, Lincoln, Nebraska 68583-0660 USA
| | - Gerrit Davidse
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166-0299 USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 371b Bond Life Sciences Center, Columbia, Missouri 65211 USA
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Dodsworth S, Chase MW, Särkinen T, Knapp S, Leitch AR. Using genomic repeats for phylogenomics: a case study in wild tomatoes (SolanumsectionLycopersicon: Solanaceae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12612] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
- Royal Botanic Gardens; Kew; Richmond; Surrey TW9 3DS UK
| | - Mark W. Chase
- Royal Botanic Gardens; Kew; Richmond; Surrey TW9 3DS UK
- School of Plant Biology; The University of Western Australia; Crawley WA 6009 Australia
| | - Tiina Särkinen
- Royal Botanic Garden, Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Sandra Knapp
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
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Kellar PR(S, Ahrendsen DL, Aust SK, Jones AR, Pires JC. Biodiversity comparison among phylogenetic diversity metrics and between three North American prairies. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400108. [PMID: 26191461 PMCID: PMC4504721 DOI: 10.3732/apps.1400108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/06/2015] [Indexed: 06/04/2023]
Abstract
Protection of Earth's ecosystems requires identification of geographical areas of greatest biodiversity. Assessment of biodiversity begins with knowledge of the evolutionary histories of species in a geographic area. Multiple phylogenetic diversity (PD) metrics have been developed to describe biodiversity beyond species counts, but sufficient empirical studies, particularly at fine phylogenetic scales, have not been conducted to provide conservation planners with evidence for incorporating PD metrics into selection of priority regions. We review notable studies that are contributing to a growing database of empirical results, we report on the effect of using high-throughput sequencing to estimate the phylogenies used to calculate PD metrics, and we discuss difficulties in selecting appropriate diversity indices. We focused on two of the most speciose angiosperm families in prairies-Asteraceae and Fabaceae-and compared 12 PD metrics and four traditional measures of biodiversity between three North American prairie sites. The varying results from the literature and from the current data reveal the wide range of applications of PD metrics and the necessity for many more empirical studies. The accumulation of results from further investigations will eventually lead to a scientific understanding upon which conservation planners can make informed decisions about where to apply limited preservation funds.
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Affiliation(s)
| | - Dakota L. Ahrendsen
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182 USA
| | - Shelly K. Aust
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182 USA
| | - Amanda R. Jones
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182 USA
| | - J. Chris Pires
- Biological Sciences, University of Missouri, 371b Bond Life Sciences Center, Columbia, Missouri 65211 USA
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Comer JR, Zomlefer WB, Barrett CF, Davis JI, Stevenson DW, Heyduk K, Leebens-Mack JH. Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing. AMERICAN JOURNAL OF BOTANY 2015; 102:888-99. [PMID: 26101415 DOI: 10.3732/ajb.1500057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/28/2015] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. METHODS Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses. KEY RESULTS Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades. CONCLUSIONS The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.
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Affiliation(s)
- Jason R Comer
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
| | - Wendy B Zomlefer
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
| | - Craig F Barrett
- California State University, Los Angeles, Department of Biological Sciences, Los Angeles, California 90032-8201 USA
| | - Jerrold I Davis
- Cornell University, Department of Plant Biology, Ithaca, New York 14853-4301 USA
| | | | - Karolina Heyduk
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
| | - James H Leebens-Mack
- University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA
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Puckett EE, Etter PD, Johnson EA, Eggert LS. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture. Mol Biol Evol 2015; 32:2338-50. [DOI: 10.1093/molbev/msv114] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Wu Z, Tembrock LR, Ge S. Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes. PLoS One 2015; 10:e0118019. [PMID: 25658309 PMCID: PMC4320078 DOI: 10.1371/journal.pone.0118019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/07/2015] [Indexed: 01/01/2023] Open
Abstract
DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.
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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
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, 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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