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Abstract
Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.
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Affiliation(s)
- Simon Creer
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, United Kingdom
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Tong W, Kim TS, Park YJ. Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing. RICE (NEW YORK, N.Y.) 2016; 9:57. [PMID: 27757948 PMCID: PMC5069220 DOI: 10.1186/s12284-016-0129-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/07/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic. RESULTS A total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. CONCLUSIONS The chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.
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Affiliation(s)
- Wei Tong
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439 Republic of Korea
| | - Tae-Sung Kim
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439 Republic of Korea
- Department of Agricultural Sciences, College of Natural Sciences, Korea National Open University, Seoul, 03087 Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439 Republic of Korea
- Center for Crop Genetic Resource and Breeding (CCGRB), Kongju National University, Cheonan, 31080 Republic of Korea
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High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus. Mol Phylogenet Evol 2016; 105:63-85. [DOI: 10.1016/j.ympev.2016.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/29/2016] [Accepted: 08/12/2016] [Indexed: 01/07/2023]
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Marcon HS, Domingues DS, Silva JC, Borges RJ, Matioli FF, Fontes MRDM, Marino CL. Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic. BMC PLANT BIOLOGY 2015; 15:198. [PMID: 26268941 PMCID: PMC4535378 DOI: 10.1186/s12870-015-0550-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/12/2015] [Indexed: 06/01/2023]
Abstract
BACKGROUND In Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. RESULTS We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values. CONCLUSION Our strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.
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Affiliation(s)
- Helena Sanches Marcon
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
| | - Douglas Silva Domingues
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil.
| | - Juliana Costa Silva
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná - IAPAR, Londrina, Brazil.
| | - Rafael Junqueira Borges
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil.
| | - Fábio Filippi Matioli
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil.
| | - Marcos Roberto de Mattos Fontes
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil.
| | - Celso Luis Marino
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil.
- Instituto de Biotecnologia da UNESP - IBTEC, Botucatu, Brazil.
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Tong W, He Q, Wang XQ, Yoon MY, Ra WH, Li F, Yu J, Oo WH, Min SK, Choi BW, Heo EB, Yun BK, Kim KW, Kim TS, Lee CY, Park YJ. A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships amongOryza sativasubspecies. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei Tong
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Qiang He
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Xiao-Qiang Wang
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Min-Young Yoon
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Won-Hee Ra
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Fengpeng Li
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Jie Yu
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Win Htet Oo
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Sun-Kyung Min
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Bu-Woong Choi
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Eun-Beom Heo
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Byoung-Kook Yun
- Department of Industrial and Systems Engineering; College of Engineering; Kongju National University; Cheonan 331-717 Korea
| | - Kyu-Won Kim
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Tae-Sung Kim
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering; College of Engineering; Kongju National University; Cheonan 331-717 Korea
| | - Yong-Jin Park
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
- Legume Bio-Resource Center of Green Manure; Kongju National University; Yesan 340-702 Korea
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Larcombe MJ, Holland B, Steane DA, Jones RC, Nicolle D, Vaillancourt RE, Potts BM. Patterns of Reproductive Isolation inEucalyptus—A Phylogenetic Perspective. Mol Biol Evol 2015; 32:1833-46. [DOI: 10.1093/molbev/msv063] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, Bossinger G, Merchant A, Udovicic F, Woodrow IE, Tibbits J. Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Mol Phylogenet Evol 2013; 69:704-16. [DOI: 10.1016/j.ympev.2013.07.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/28/2013] [Accepted: 07/08/2013] [Indexed: 12/01/2022]
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Ramadugu C, Pfeil BE, Keremane ML, Lee RF, Maureira-Butler IJ, Roose ML. A six nuclear gene phylogeny of Citrus (Rutaceae) taking into account hybridization and lineage sorting. PLoS One 2013; 8:e68410. [PMID: 23874615 PMCID: PMC3713030 DOI: 10.1371/journal.pone.0068410] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 05/29/2013] [Indexed: 12/14/2022] Open
Abstract
Background Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species. Methodology and Principal Findings (1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test. Conclusions We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus.
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Affiliation(s)
- Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Bernard E. Pfeil
- Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory, Australia
- DBES, Gothenburg University, Gothenburg, Sweden
- * E-mail:
| | - Manjunath L. Keremane
- United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America
| | - Richard F. Lee
- United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America
| | - Ivan J. Maureira-Butler
- Agriaquaculture Nutritional Genomic Center, Centro de Genómica Nutricional Agroacuícola, Genomics and Bioinformatics Unit, Temuco, Chile
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
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Waters DLE, Nock CJ, Ishikawa R, Rice N, Henry RJ. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecol Evol 2012; 2:211-7. [PMID: 22408737 PMCID: PMC3297189 DOI: 10.1002/ece3.66] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/30/2011] [Accepted: 10/03/2011] [Indexed: 12/16/2022] Open
Abstract
Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.
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Blanco-Pastor JL, Vargas P, Pfeil BE. Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria. PLoS One 2012; 7:e39089. [PMID: 22768061 PMCID: PMC3387178 DOI: 10.1371/journal.pone.0039089] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/18/2012] [Indexed: 11/21/2022] Open
Abstract
We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora.
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Affiliation(s)
- José Luis Blanco-Pastor
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Madrid, Spain.
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Dickinson GR, Lee DJ, Wallace HM. The influence of pre- and post-zygotic barriers on interspecific Corymbia hybridization. ANNALS OF BOTANY 2012; 109:1215-26. [PMID: 22419764 PMCID: PMC3359913 DOI: 10.1093/aob/mcs050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Corymbia species from different sections hybridize readily, with some of increasing economic importance to plantation forestry. This study explores the locations of reproductive barriers between interspecific Corymbia hybrids and investigates the reproductive success of a wide taxonomic range of C. torelliana hybrid crosses. METHODS Pollen, pistil and embryo development were investigated for four C. torelliana crosses (×C. torelliana, ×C. citriodora subsp. citriodora, ×C. tessellaris and ×C. intermedia) using fluorescent and standard microscopy to identify the locations of interspecific reproductive isolating barriers. Corymbia torelliana was also crossed with 16 taxa, representing six of the seven Corymbia sections, both Corymbia subgenera and one species each from the related genera, Angophora and Eucalyptus. All crosses were assessed for capsule and seed yields. KEY RESULTS Interspecific C. torelliana hybridization was controlled by pre-zygotic reproductive isolating barriers inhibiting pollen adhesion to the stigma, pollen germination, pollen tube growth in the style and pollen tube penetration of the micropyle. Corymbia torelliana (subgenus Blakella, sect. Torellianae) was successfully hybridized with Corymbia species from subgenus Blakella, particularly C. citriodora subsp. citriodora, C. citriodora subsp. variegata, C. henryi (sect. Maculatae) and C. tessellaris (sect. Abbreviatae), and subgenus Corymbia, particularly C. clarksoniana and C. erythrophloia (sect. Septentrionales). Attempted intergeneric hybrids between C. torelliana and either Angophora floribunda or Eucalyptus pellita were unsuccessful. CONCLUSIONS Corymbia hybrids were formed between species from different sections and subgenera, but not with species from the related genera Angophora or Eucalyptus. Reproductive isolation between the interspecific Corymbia hybrid crosses was controlled by early- and late-acting pre-zygotic isolating barriers, with reproductive success generally decreasing with increasing taxonomic distance between parent species. These findings support the monophyly of Corymbia and the close relationships of infrageneric clades. The hybridizing propensity of Corymbia species provides opportunities for breeding but suggests risks of environmental gene flow.
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Affiliation(s)
- Geoffrey R Dickinson
- Agri-Science Queensland, Department of Employment, Economic Development and Innovation, Mareeba, Queensland 4880, Australia.
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Zheng X, Hu C, Spooner D, Liu J, Cao J, Teng Y. Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae). BMC Evol Biol 2011; 11:255. [PMID: 21917170 PMCID: PMC3182939 DOI: 10.1186/1471-2148-11-255] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 09/14/2011] [Indexed: 12/03/2022] Open
Abstract
Background The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility. Results DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N. Conclusions Our study represents the first phylogenetic analyses based on LCNGs in Pyrus. Ancient and recent duplications lead to a complex structure of Adh outparalogs and inparalogs in Pyrus and Malus, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, LFY2int2-N is the best nuclear marker for phylogenetic reconstruction of Pyrus due to suitable sequence divergence and the absence of lineage sorting.
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Affiliation(s)
- Xiaoyan Zheng
- Department of Horticulture, State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Barakat A, Yassin NBM, Park JS, Choi A, Herr J, Carlson JE. Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:249-57. [PMID: 21763535 DOI: 10.1016/j.plantsci.2011.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/16/2011] [Accepted: 05/17/2011] [Indexed: 05/08/2023]
Abstract
The biosynthesis of monolignols, the main components of lignin, involves many intermediates and enzymes. The cinnamoyl-CoA reductase (CCR) enzyme catalyzes the conversion of cinnamoyl-CoAs to cinnamaldehydes, i.e. the first specific step in lignin synthesis. The CCR and CCR-like gene family was studied partially in several plant species. This is a comprehensive study of the CCR and CCR-like gene family including genome organization, gene structure, phylogeny across land plant species, and, expression profiling in Populus. Analysis of amino acid motifs enabled the identification of sequence variations in the CCR catalytic site and annotates CCR and CCR-like genes. CCR and CCR-like genes were distributed in three major phylogenetic classes of which one includes the bona fide CCR genes. The other two classes include CCR and CCR-like, of which several genes present a high similarity to cinnamyl alcohol dehydrogenase, or dihydroflavonol reductase (DFR) genes. All CCR, CCR-like, and DFR classes were deeply rooted in the phylogeny of land plants suggesting that their evolution preceded the evolution of lycophytes. Over two thirds of CCR and CCR-like Populus genes were physically distributed on duplicated regions. This suggests that these duplication/retention processes contributed significantly to the size of the CCR and CCR-like gene family. The Populus CCR and CCR-like genes showed six expression patterns in the tissues studied with a preferential expression of PoptrCCR12 in xylem. The other genes present divergent expression profiles with some preferentially expressed in leaves, bark, or both. Several CCR and CCR-like genes were induced or repressed under various abiotic stresses suggesting that their duplication was followed by the evolution of divergent expression profiles and divergence of functions.
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Affiliation(s)
- Abdelali Barakat
- The Department of Bioenergy Science & Technology. Chonnam National University, Buk-Gu, Gwangju, 500-757, Republic of Korea.
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Steane DA, Nicolle D, Sansaloni CP, Petroli CD, Carling J, Kilian A, Myburg AA, Grattapaglia D, Vaillancourt RE. Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping. Mol Phylogenet Evol 2011; 59:206-24. [PMID: 21310251 DOI: 10.1016/j.ympev.2011.02.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 02/01/2011] [Accepted: 02/02/2011] [Indexed: 11/30/2022]
Abstract
A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.
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Affiliation(s)
- Dorothy A Steane
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia.
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Brokaw JM, Hufford L. Origins and introgression of polyploid species in Mentzelia section Trachyphytum (Loasaceae). AMERICAN JOURNAL OF BOTANY 2010; 97:1457-1473. [PMID: 21616900 DOI: 10.3732/ajb.0900388] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Polyploid speciation has been important in plant evolution. However, the conditions that favor the origination and persistence of polyploids are still not well understood. Here, we examine origins of 16 polyploid species in Mentzelia section Trachyphytum. • METHODS We used phylogeny reconstructions based on DNA sequences from plastid regions and the nuclear gene isocitrate dehydrogenase (idh) to construct hypotheses of introgression and polyploidization. • KEY RESULTS Molecular data suggest that homoploid hybridization has been surprisingly common in Trachyphytum. Diploid species had unequal involvement in polyploid origins, but most polyploid taxa had allopolyploid origins from extant progenitors. A few polyploids with extreme phenotypes did not appear to have extant progenitors. We infer that the progenitors of these species were derived from extinct diploid lineages or ancestral lineages of multiple extant diploids. In agreement with other recent studies, we recovered molecular evidence of multiple phylogenetically distinct origins for several polyploid taxa, including the widespread octoploid M. albicaulis. • CONCLUSIONS Evidence of high levels of introgression and allopolyploidy suggests that hybridization has played an important role in the evolution of Trachyphytum. Although idh sequences exhibited complicated evolution, including gene duplication, deletion, and recombination, they provided a higher percentage of informative characters for phylogeny reconstruction than the most variable plastid regions, allowing tests of hypotheses regarding polyploid origins. Given the necessity for rapidly evolving low-copy nuclear genes, researchers studying hybridization and polyploidy may increasingly turn to complex sequence data.
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Affiliation(s)
- Joshua M Brokaw
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236 USA
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Frajman B, Eggens F, Oxelman B. Hybrid Origins and Homoploid Reticulate Evolution within Heliosperma (Sileneae, Caryophyllaceae)—A Multigene Phylogenetic Approach with Relative Dating. Syst Biol 2009; 58:328-45. [DOI: 10.1093/sysbio/syp030] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Božo Frajman
- Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
- Biology Department, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Frida Eggens
- Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Bengt Oxelman
- Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
- Department of Plant and Environmental Sciences, Göteborg University, Box 461, SE-405 30 Göteborg, Sweden; E-mail:
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Li M, Wunder J, Bissoli G, Scarponi E, Gazzani S, Barbaro E, Saedler H, Varotto C. Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics 2008. [DOI: 10.1111/j.1096-0031.2008.00207.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Cook LG, Morris DC, Edwards RD, Crisp MD. Reticulate evolution in the natural range of the invasive wetland tree species Melaleuca quinquenervia. Mol Phylogenet Evol 2008; 47:506-22. [DOI: 10.1016/j.ympev.2008.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 01/21/2008] [Accepted: 02/14/2008] [Indexed: 11/17/2022]
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Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)? Mol Phylogenet Evol 2008; 48:313-25. [PMID: 18490181 DOI: 10.1016/j.ympev.2008.04.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 04/04/2008] [Accepted: 04/07/2008] [Indexed: 11/23/2022]
Abstract
Despite sampling of up to 25kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable phylogenetic hypothesis in these parts of the tree. The main reason for this is probably a combination of rapid radiation and substitution rate heterogeneity. Poor resolution among closely related species are often explained by low levels of variation in chloroplast data, but the problem with our data appear to be high levels of homoplasy. Tree-like cpDNA evolution cannot be rejected, but apparent incongruent patterns between different regions are evaluated with the possibility of ancient interspecific chloroplast recombination as explanatory model. However, several major phylogenetic relationships, previously not recognized, are confidently resolved, e.g. the grouping of the two SW Anatolian taxa S. cryptoneura and S. sordida strongly disagrees with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. The closely related S. atocioides and S. aegyptiaca form a sister group to Lychnis and the rest of Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data.
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Bayly MJ, Udovicic F, Gibbs AK, Parra-O. C, Ladiges PY. Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysis. Cladistics 2008. [DOI: 10.1111/j.1096-0031.2007.00175.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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McKinnon GE, Vaillancourt RE, Steane DA, Potts BM. An AFLP marker approach to lower-level systematics in Eucalyptus (Myrtaceae). AMERICAN JOURNAL OF BOTANY 2008; 95:368-380. [PMID: 21632361 DOI: 10.3732/ajb.95.3.368] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Genus Eucalyptus, with over 700 species, presents a number of systematic difficulties including taxa that hybridize or intergrade across environmental gradients. To date, no DNA marker has been found capable of resolving phylogeny below the sectional level in the major subgenera. Molecular markers are needed to support taxonomic revision, assess the extent of genetic divergence at lower taxonomic levels, and inform conservation efforts. We examined the utility of 930 amplified fragment length polymorphisms (AFLPs) for analyzing relationships among Tasmanian taxa of subgenus Symphyomyrtus section Maidenaria. Phenetic and cladistic analyses resolved species into clusters demonstrating significant genetic partitioning, largely concordant with series defined in the most recent taxonomic revision of Eucalyptus. Some departures from current taxonomy were noted, indicating possible cases of morphological convergence and character reversion. Although the resolution obtained using AFLP was greatly superior to that of single sequence markers, the data demonstrated high homoplasy and incomplete resolution of closely related species. The results of this study and others are consistent with recent speciation and reticulate evolution in Maidenaria. We conclude that a combination of phylogenetic and population genetic approaches using multiple molecular markers offers the best prospects for understanding taxonomic relationships below the sectional level in Eucalyptus.
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Bayly MJ, Ladiges PY. Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae). Mol Phylogenet Evol 2007; 44:346-56. [DOI: 10.1016/j.ympev.2006.10.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/09/2006] [Accepted: 10/23/2006] [Indexed: 10/23/2022]
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Scheffler K, Martin DP, Seoighe C. Robust inference of positive selection from recombining coding sequences. Bioinformatics 2006; 22:2493-9. [PMID: 16895925 DOI: 10.1093/bioinformatics/btl427] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Accurate detection of positive Darwinian selection can provide important insights to researchers investigating the evolution of pathogens. However, many pathogens (particularly viruses) undergo frequent recombination and the phylogenetic methods commonly applied to detect positive selection have been shown to give misleading results when applied to recombining sequences. We propose a method that makes maximum likelihood inference of positive selection robust to the presence of recombination. This is achieved by allowing tree topologies and branch lengths to change across detected recombination breakpoints. Further improvements are obtained by allowing synonymous substitution rates to vary across sites. RESULTS Using simulation we show that, even for extreme cases where recombination causes standard methods to reach false positive rates >90%, the proposed method decreases the false positive rate to acceptable levels while retaining high power. We applied the method to two HIV-1 datasets for which we have previously found that inference of positive selection is invalid owing to high rates of recombination. In one of these (env gene) we still detected positive selection using the proposed method, while in the other (gag gene) we found no significant evidence of positive selection. AVAILABILITY A HyPhy batch language implementation of the proposed methods and the HIV-1 datasets analysed are available at http://www.cbio.uct.ac.za/pub_support/bioinf06. The HyPhy package is available at http://www.hyphy.org, and it is planned that the proposed methods will be included in the next distribution. RDP2 is available at http://darwin.uvigo.es/rdp/rdp.html
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Affiliation(s)
- Konrad Scheffler
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine University of Cape Town, Private Bag, Rondebosch 7701, South Africa.
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