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Yang Y, Zhou T, Duan D, Yang J, Feng L, Zhao G. Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species. FRONTIERS IN PLANT SCIENCE 2016; 7:959. [PMID: 27446185 PMCID: PMC4923075 DOI: 10.3389/fpls.2016.00959] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/15/2016] [Indexed: 05/08/2023]
Abstract
Quercus is considered economically and ecologically one of the most important genera in the Northern Hemisphere. Oaks are taxonomically perplexing because of shared interspecific morphological traits and intraspecific morphological variation, which are mainly attributed to hybridization. Universal plastid markers cannot provide a sufficient number of variable sites to explore the phylogeny of this genus, and chloroplast genome-scale data have proven to be useful in resolving intractable phylogenetic relationships. In this study, the complete chloroplast genomes of four Quercus species were sequenced, and one published chloroplast genome of Quercus baronii was retrieved for comparative analyses. The five chloroplast genomes ranged from 161,072 bp (Q. baronii) to 161,237 bp (Q. dolicholepis) in length, and their gene organization and order, and GC content, were similar to those of other Fagaceae species. We analyzed nucleotide substitutions, indels, and repeats in the chloroplast genomes, and found 19 relatively highly variable regions that will potentially provide plastid markers for further taxonomic and phylogenetic studies within Quercus. We observed that four genes (ndhA, ndhK, petA, and ycf1) were subject to positive selection. The phylogenetic relationships of the Quercus species inferred from the chloroplast genomes obtained moderate-to-high support, indicating that chloroplast genome data may be useful in resolving relationships in this genus.
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Affiliation(s)
| | | | | | | | | | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi’an, China
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 756] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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53
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Janssens SB, Vandelook F, De Langhe E, Verstraete B, Smets E, Vandenhouwe I, Swennen R. Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia. THE NEW PHYTOLOGIST 2016; 210:1453-65. [PMID: 26832306 PMCID: PMC5066818 DOI: 10.1111/nph.13856] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/07/2015] [Indexed: 05/20/2023]
Abstract
Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species-rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo-Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera - Ensete, Musa and Musella - originated in northern Indo-Burma during the early Eocene. Musa species dispersed from 'northwest to southeast' into Southeast Asia with only few back-dispersals towards northern Indo-Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.
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Affiliation(s)
| | | | - Edmond De Langhe
- Laboratory of Tropical Crop ImprovementWillem de Croylaan 42LeuvenBE‐3001Belgium
| | | | - Erik Smets
- Plant Conservation and Population BiologyKU LeuvenKasteelpark Arenberg 31PO Box 2435LeuvenBE‐3001Belgium
- Naturalis Biodiversity CenterLeiden UniversityPO Box 9517Leiden2300RAthe Netherlands
| | - Ines Vandenhouwe
- Bioversity InternationalWillem De Croylaan 42LeuvenBE‐3001Belgium
| | - Rony Swennen
- Laboratory of Tropical Crop ImprovementWillem de Croylaan 42LeuvenBE‐3001Belgium
- Bioversity InternationalWillem De Croylaan 42LeuvenBE‐3001Belgium
- International Institute of Tropical AgriculturePO Box 10, DulutiArushaTanzania
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54
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Lim GS, Barrett CF, Pang CC, Davis JI. Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri. AMERICAN JOURNAL OF BOTANY 2016; 103:1129-37. [PMID: 27335389 DOI: 10.3732/ajb.1600042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/06/2016] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Heterotrophic angiosperms tend to have reduced plastome sizes relative to those of their autotrophic relatives because genes that code for proteins involved in photosynthesis are lost. However, some plastid-encoded proteins may have vital nonphotosynthetic functions, and the plastome therefore may be retained after the loss of photosynthesis. METHODS We sequenced the plastome of the mycoheterotrophic species Thismia tentaculata and a representative of its sister genus, Tacca chantrieri, using next-generation technology, and we compared sequences and structures of genes and genomes of these species. KEY RESULTS The plastome of Tacca chantrieri is similar to those of other autotrophic taxa of Dioscoreaceae, except in a few local rearrangements and one gene loss. The plastome of Thismia tentaculata is ca. 16 kbp long with a quadripartite structure and is among the smallest known plastomes. Synteny is minimal between the plastomes of Tacca chantrieri and Thismia tentaculata. The latter includes only 12 candidate genes, with all except accD involved in protein synthesis. Of the 12 genes, trnE, trnfM, and accD are frequently among the few that remain in depauperate plastomes. CONCLUSIONS The plastome of Thismia tentaculata, like those of most other heterotrophic plants, includes a small number of genes previously suggested to be essential to plastome survival.
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Affiliation(s)
- Gwynne S Lim
- The New York Botanical Garden, Pfizer Plant Research Laboratory, 2900 Southern Boulevard, Bronx, New York 10458 USA L. H. Bailey Hortorium, Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, New York 14853 USA
| | - Craig F Barrett
- Department of Biology, Life Sciences Building, PO Box 6057, Morgantown, West Virginia 26506 USA
| | - Chun-Chiu Pang
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jerrold I Davis
- L. H. Bailey Hortorium, Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, New York 14853 USA
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Givnish TJ, Zuluaga A, Marques I, Lam VKY, Gomez MS, Iles WJD, Ames M, Spalink D, Moeller JR, Briggs BG, Lyon SP, Stevenson DW, Zomlefer W, Graham SW. Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica. Cladistics 2016; 32:581-605. [DOI: 10.1111/cla.12153] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Thomas J. Givnish
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Alejandro Zuluaga
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
- Departamento de Biología; Universidad del Valle; Cali Colombia
| | - Isabel Marques
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
- Department of Agriculture (Botany); High Polytechnic School of Huesca; University of Zaragoza; Carretera de Cuarte Km 1 Huesca E22071 Spain
| | - Vivienne K. Y. Lam
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
| | - Marybel Soto Gomez
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
| | - William J. D. Iles
- University and Jepson Herbaria; University of California-Berkeley; Berkeley CA 94720 USA
| | - Mercedes Ames
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Daniel Spalink
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Jackson R. Moeller
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | | | - Stephanie P. Lyon
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | | | - Wendy Zomlefer
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | - Sean W. Graham
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
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Luo Y, Ma PF, Li HT, Yang JB, Wang H, Li DZ. Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales. Genome Biol Evol 2016; 8:932-45. [PMID: 26957030 PMCID: PMC4823975 DOI: 10.1093/gbe/evv260] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2015] [Indexed: 01/03/2023] Open
Abstract
The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatales tree precludes answering questions about the early evolution of the order. Here, we sequenced the first complete plastid genomes from three key families in this order:Potamogeton perfoliatus(Potamogetonaceae),Sagittaria lichuanensis(Alismataceae), andTofieldia thibetica(Tofieldiaceae). Each family possesses the typical quadripartite structure, with plastid genome sizes of 156,226, 179,007, and 155,512 bp, respectively. Among them, the plastid genome ofS. lichuanensisis the largest in monocots and the second largest in angiosperms. Like other sequenced Alismatales plastid genomes, all three families generally encode the same 113 genes with similar structure and arrangement. However, we detected 2.4 and 6 kb inversions in the plastid genomes ofSagittariaandPotamogeton, respectively. Further, we assembled a 79 plastid protein-coding gene sequence data matrix of 22 taxa that included the three newly generated plastid genomes plus 19 previously reported ones, which together represent all primary lineages of monocots and outgroups. In plastid phylogenomic analyses using maximum likelihood and Bayesian inference, we show both strong support for Acorales as sister to the remaining monocots and monophyly of Alismatales. More importantly, Tofieldiaceae was resolved as the most basal lineage within Alismatales. These results provide new insights into the evolution of Alismatales as well as the early-diverging monocots as a whole.
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Affiliation(s)
- Yang Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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57
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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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58
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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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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: 84] [Impact Index Per Article: 9.3] [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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Redwan RM, Saidin A, Kumar SV. Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae. BMC PLANT BIOLOGY 2015; 15:196. [PMID: 26264372 PMCID: PMC4534033 DOI: 10.1186/s12870-015-0587-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/03/2015] [Indexed: 05/13/2023]
Abstract
BACKGROUND Pineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology. RESULTS In this study, the high error rate of PacBio long sequence reads of A. comosus's total genomic DNA were improved by leveraging on the high accuracy but short Illumina reads for error-correction via the latest error correction module from Novocraft. Error corrected long PacBio reads were assembled by using a single tool to produce a contig representing the pineapple chloroplast genome. The genome of 159,636 bp in length is featured with the conserved quadripartite structure of chloroplast containing a large single copy region (LSC) with a size of 87,482 bp, a small single copy region (SSC) with a size of 18,622 bp and two inverted repeat regions (IRA and IRB) each with the size of 26,766 bp. Overall, the genome contained 117 unique coding regions and 30 were repeated in the IR region with its genes contents, structure and arrangement similar to its sister taxon, Typha latifolia. A total of 35 repeats structure were detected in both the coding and non-coding regions with a majority being tandem repeats. In addition, 205 SSRs were detected in the genome with six protein-coding genes contained more than two SSRs. Comparative chloroplast genomes from the subclass Commelinidae revealed a conservative protein coding gene albeit located in a highly divergence region. Analysis of selection pressure on protein-coding genes using Ka/Ks ratio showed significant positive selection exerted on the rps7 gene of the pineapple chloroplast with P less than 0.05. Phylogenetic analysis confirmed the recent taxonomical relation among the member of commelinids which support the monophyly relationship between Arecales and Dasypogonaceae and between Zingiberales to the Poales, which includes the A. comosus. CONCLUSIONS The complete sequence of the chloroplast of pineapple provides insights to the divergence of genic chloroplast sequences from the members of the subclass Commelinidae. The complete pineapple chloroplast will serve as a reference for in-depth taxonomical studies in the Bromeliaceae family when more species under the family are sequenced in the future. The genetic sequence information will also make feasible other molecular applications of the pineapple chloroplast for plant genetic improvement.
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Affiliation(s)
- R M Redwan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - A Saidin
- Novocraft Technology Sdn. Bhd., 3 Two Square, Seksyen 19, Petaling Jaya, Selangor, Malaysia.
| | - S V Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
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Lam VKY, Soto Gomez M, Graham SW. The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection. Genome Biol Evol 2015; 7:2220-36. [PMID: 26170229 PMCID: PMC4558852 DOI: 10.1093/gbe/evv134] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2015] [Indexed: 11/14/2022] Open
Abstract
The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.
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Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
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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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Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. AOB PLANTS 2015; 7:plv046. [PMID: 25940204 PMCID: PMC4480051 DOI: 10.1093/aobpla/plv046] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/21/2015] [Indexed: 05/08/2023]
Abstract
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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Affiliation(s)
- Jeffery M Saarela
- Botany Section, Research and Collections, Canadian Museum of Nature, PO Box 3443 Stn. D, Ottawa, ON, Canada K1P 3P4
| | - William P Wysocki
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Craig F Barrett
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA 90032-8201, USA
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jerrold I Davis
- Section of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
| | - Lynn G Clark
- Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, USA
| | - Scot A Kelchner
- Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dustin R Mayfield
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
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Harrup LE, Bellis GA, Balenghien T, Garros C. Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: current challenges and future directions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:249-266. [PMID: 25535946 PMCID: PMC4330985 DOI: 10.1016/j.meegid.2014.12.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 11/23/2022]
Abstract
Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.
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Affiliation(s)
- L E Harrup
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.
| | - G A Bellis
- University of Queensland, St Lucia, Brisbane, Qld, Australia
| | - T Balenghien
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
| | - C Garros
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
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Dodsworth S, Chase MW, Kelly LJ, Leitch IJ, Macas J, Novák P, Piednoël M, Weiss-Schneeweiss H, Leitch AR. Genomic repeat abundances contain phylogenetic signal. Syst Biol 2015; 64:112-26. [PMID: 25261464 PMCID: PMC4265144 DOI: 10.1093/sysbio/syu080] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
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Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mark W Chase
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Ilia J Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jiří Macas
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Petr Novák
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mathieu Piednoël
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Vaughn JN, Chaluvadi SR, Tushar, Rangan L, Bennetzen JL. Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology. PLoS One 2014; 9:e108581. [PMID: 25333869 PMCID: PMC4204815 DOI: 10.1371/journal.pone.0108581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/28/2014] [Indexed: 11/19/2022] Open
Abstract
Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family.
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Affiliation(s)
- Justin N. Vaughn
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Srinivasa R. Chaluvadi
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Tushar
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Latha Rangan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
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Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Mol Biol Evol 2014; 31:3095-112. [PMID: 25172958 DOI: 10.1093/molbev/msu252] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Parasitic organisms exemplify morphological and genomic reduction. Some heterotrophic, parasitic plants harbor drastically reduced and degraded plastid genomes resulting from relaxed selective pressure on photosynthetic function. However, few studies have addressed the initial stages of plastome degradation in groups containing both photosynthetic and nonphotosynthetic species. Corallorhiza is a genus of leafless, heterotrophic orchids that contains both green, photosynthetic species and nongreen, putatively nonphotosynthetic species, and represents an ideal system in which to assess the beginning of the transition to a "minimal plastome." Complete plastomes were generated for nine taxa of Corallorhiza using Illumina paired-end sequencing of genomic DNA to assess the degree of degradation among taxa, and for comparison with a general model of degradation among angiosperms. Quantification of total chlorophyll suggests that nongreen Corallorhiza still produce chlorophyll, but at 10-fold lower concentrations than green congeners. Complete plastomes and partial nuclear rDNA cistrons yielded a fully resolved tree for Corallorhiza, with at least two independent losses of photosynthesis, evidenced by gene deletions and pseudogenes in Co. striata and nongreen Co. maculata. All Corallorhiza show some evidence of degradation in genes of the NAD(P)H dehydrogenase complex. Among genes with open reading frames, photosynthesis-related genes displayed evidence of neutral evolution in nongreen Corallorhiza, whereas genes of the ATP synthase complex displayed some evidence of positive selection in these same groups, though for reasons unknown. Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastome evolution in heterotrophic angiosperms.
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Affiliation(s)
- Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles
| | - John V Freudenstein
- Department of Evolution, Ecology, and Organismal Biology and the Museum of Biological Diversity, Ohio State University
| | - Jeff Li
- Department of Biological Sciences, California State University, Los Angeles
| | | | - Leticia Perez
- Department of Biological Sciences, California State University, Los Angeles
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri
| | - Cristian Santos
- Department of Biological Sciences, California State University, Los Angeles
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Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Mol Phylogenet Evol 2014; 80:169-85. [PMID: 25109653 DOI: 10.1016/j.ympev.2014.07.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 11/21/2022]
Abstract
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.
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Ma PF, Zhang YX, Zeng CX, Guo ZH, Li DZ. Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae). Syst Biol 2014; 63:933-50. [DOI: 10.1093/sysbio/syu054] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Peng-Fei Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Xiao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Chun-Xia Zeng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhen-Hua Guo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; 2Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; and 3Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Liu Y, Cox CJ, Wang W, Goffinet B. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Syst Biol 2014; 63:862-78. [PMID: 25070972 DOI: 10.1093/sysbio/syu049] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cymon J Cox
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, Kougbeadjo A, Maillol V, Martin G, Sabot F, Santoni S, Vigouroux Y, Couvreur TLP. Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol Ecol Resour 2014; 14:1103-13. [DOI: 10.1111/1755-0998.12258] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Cédric Mariac
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Nora Scarcelli
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Juliette Pouzadou
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Adeline Barnaud
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Laboratoire National de Recherche sur les Productions Végétales; Institut Sénégalais de Recherches Agricoles; Centre de Recherche de Bel Air; Dakar Senegal
- Laboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress Environnementaux; Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop; Centre de Recherche de Bel Air; Dakar Senegal
| | | | - Adama Faye
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Université de Yaoundé I; Ecole Normale Supérieure; Département des Sciences Biologiques; Laboratoire de Botanique; Systématique et d'Ecologie; B.P.047 Yaoundé Cameroon
| | - Ayite Kougbeadjo
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Vincent Maillol
- UMR AGAP; Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; INRA; 2 Place Viala 34060 Montpellier France
| | | | - François Sabot
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Sylvain Santoni
- UMR AGAP; Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; INRA; 2 Place Viala 34060 Montpellier France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Thomas L. P. Couvreur
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Université de Yaoundé I; Ecole Normale Supérieure; Département des Sciences Biologiques; Laboratoire de Botanique; Systématique et d'Ecologie; B.P.047 Yaoundé Cameroon
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Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 2014; 14:23. [PMID: 24533922 PMCID: PMC3933183 DOI: 10.1186/1471-2148-14-23] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/13/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. RESULTS We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. CONCLUSIONS Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475, USA
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Affiliation(s)
- Leandro C S Assis
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Leandro M Santos
- Laboratório de Biologia Comparada de Hymenoptera, Departamento de Zoologia, Universidade Federal do Paraná, Caixa Postal 19020, Curitiba, PR, 81531-980, Brazil.,Programa de Pós-Graduação em Entomologia, bolsista do CNPq
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Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI. Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)? ANNALS OF BOTANY 2014; 113:119-33. [PMID: 24280362 PMCID: PMC3864734 DOI: 10.1093/aob/mct264] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/16/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. METHODS Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support. KEY RESULTS Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies. CONCLUSIONS Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.
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Affiliation(s)
- Craig F. Barrett
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Chelsea D. Specht
- Departments of Plant and Microbial Biology and Integrative Biology, The University and Jepson Herbaria, University of California, Berkeley CA 94720, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jerrold I. Davis
- Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
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Logacheva MD, Schelkunov MI, Nuraliev MS, Samigullin TH, Penin AA. The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements. Genome Biol Evol 2014; 6:238-46. [PMID: 24398375 PMCID: PMC3914687 DOI: 10.1093/gbe/evu001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 12/31/2022] Open
Abstract
Plastid genomes of nonphotosynthetic plants represent a perfect model for studying evolution under relaxed selection pressure. However, the information on their sequences is still limited. We sequenced and assembled plastid genome of Petrosavia stellaris, a rare mycoheterotrophic monocot plant. After orchids, Petrosavia represents only the second family of nonphotosynthetic monocots to have its plastid genome examined. Several unusual features were found: retention of the ATP synthase genes and rbcL gene; extensive gene order rearrangement despite a relative lack of repeat sequences; an unusually short inverted repeat region that excludes most of the rDNA operon; and a lack of evidence for accelerated sequence evolution. Plastome of photosynthetic relative of P. stellaris, Japonolirion osense, has standard gene order and does not have the predisposition to inversions. Thus, the rearrangements in the P. stellaris plastome are the most likely associated with transition to heterotrophic way of life.
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Affiliation(s)
- Maria D. Logacheva
- M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail I. Schelkunov
- M.V. Lomonosov Moscow State University, Moscow, Russia
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maxim S. Nuraliev
- M.V. Lomonosov Moscow State University, Moscow, Russia
- Joint Russian–Vietnamese Tropical Scientific and Technological Center, Cau Giay, Hanoi, Vietnam
| | | | - Aleksey A. Penin
- M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
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Huang YY, Matzke AJM, Matzke M. Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS One 2013; 8:e74736. [PMID: 24023703 PMCID: PMC3758300 DOI: 10.1371/journal.pone.0074736] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/06/2013] [Indexed: 11/29/2022] Open
Abstract
Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.
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Affiliation(s)
- Ya-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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