1
|
Han MJ, Xu HE, Xiong XM, Zhang HH. Evolutionary dynamics of transposable elements during silkworm domestication. Genes Genomics 2018; 40:1041-1051. [DOI: 10.1007/s13258-018-0713-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/31/2018] [Indexed: 11/24/2022]
|
2
|
Boltenkov EV, Artyukova EV, Kozyrenko MM. Species divergence in Iris series Lacteae (Iridaceae) in Russia and adjacent countries based on chloroplast DNA sequence data. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Ying LX, Zhang TT, Chiu CA, Chen TY, Luo SJ, Chen XY, Shen ZH. The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations. Ecol Evol 2016; 6:2805-16. [PMID: 27066254 PMCID: PMC4801808 DOI: 10.1002/ece3.2042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/04/2022] Open
Abstract
The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy–Weinberg equilibrium, with a genetic differentiation parameter of Rst of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation‐by‐distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (Gst = 0.712) among populations. A high Gst of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long‐term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F. hayatae and other Chinese beech species.
Collapse
Affiliation(s)
- Ling-Xiao Ying
- Department of Ecology College of Urban and Environmental Sciences The MOE Key Laboratory of Earth Surface Processes Peking University Beijing 100871 China
| | - Ting-Ting Zhang
- School of Life Sciences Peking-Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Ching-An Chiu
- Experimental Forest/Department of Forestry National Chung Hsing University 250 Kuokuang Rd. Taichung 40227
| | - Tze-Ying Chen
- Department of Forestry and Natural Resources National Ilan University 1 Sec. 1 Shen-Lung Road I-Lan 260
| | - Shu-Jin Luo
- School of Life Sciences Peking-Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Xiao-Yong Chen
- College of Natural Resource and Environment East China Normal University Shanghai 200062 China
| | - Ze-Hao Shen
- Department of Ecology College of Urban and Environmental Sciences The MOE Key Laboratory of Earth Surface Processes Peking University Beijing 100871 China
| |
Collapse
|
4
|
Alonso C, Herrera CM. Back-and-forth hermaphroditism: phylogenetic context of reproductive system evolution in subdioecious Daphne laureola. Evolution 2011; 65:1680-92. [PMID: 21644956 DOI: 10.1111/j.1558-5646.2011.01246.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent phylogenetic analyses of sexual reproductive systems supported the evolutionary pathway from hermaphroditism to dioecy via gynodioecy in different groups of angiosperms. In this study, we explore the evolution of sexual reproductive systems in Daphne laureola L. (Thymelaeaceae), a species with variation in reproductive system among population. Sequences from the ITS region of the nuclear ribosomal cistron and two plastid markers (psbA-trnH and ndhF) were analyzed and used to map the population reproductive system along the molecular phylogeny. Our results support D. laureola as a monophyletic lineage with three different clades within the Iberian Peninsula. The hermaphroditic populations belong to two different clades, whereas gynodioecy is ubiquitous but characteristic of the third clade, which grouped together all the North-Western Iberian populations sampled, including the apparently oldest haplotype sampled. Gynodioecy appears as the most likely basal condition of the 13 analyzed populations, but different evolutionary transitions in reproductive sexual system were traced within each D. laureola clade. Both ecological conditions and (meta)population dynamics may help explain plant reproductive system evolution at the microevolutionary scale. Phylogenetic studies in which the historical relationships between populations differing in reproductive system can be ascertained will help to clarify the process.
Collapse
Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas Apdo 1056, 41080 Sevilla, Spain.
| | | |
Collapse
|
5
|
Lockton S, Gaut BS. The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol 2010; 10:10. [PMID: 20067644 PMCID: PMC2837042 DOI: 10.1186/1471-2148-10-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 01/12/2010] [Indexed: 12/02/2022] Open
Abstract
Background Transposable Elements (TEs) make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. Plant reproductive systems are diverse and mating type variation is one factor among many hypothesized to influence TE evolutionary dynamics. Here, we collected a large TE-display data set in self-fertilizing Arabidopsis thaliana, and compared it to data gathered in outcrossing Arabidopsis lyrata. We analyzed seven TE families in four natural populations of each species to tease apart the effects of mating system, demography, transposition, and selection in determining patterns of TE diversity. Results Measures of TE band differentiation were largely consistent across TE families. However, patterns of diversity in A. thaliana Ac elements differed significantly from that other TEs, perhaps signaling a lack of recent transposition. Across TE families, we estimated higher allele frequencies and lower selection coefficients on A. thaliana TE insertions relative to A. lyrata TE insertions. Conclusions The differences in TE distributions between the two Arabidopsis species represents a synthesis of evolutionary forces that include the transposition dynamics of individual TE families and the demographic histories of populations. There are also species-specific differences that could be attributed to the effects of mating system, including higher overall allele frequencies in the selfing lineage and a greater proportion of among population TE diversity in the outcrossing lineage.
Collapse
Affiliation(s)
- Steven Lockton
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA.
| | | |
Collapse
|
6
|
Kozyrenko MM, Artyukova EV, Zhuravlev YN. Independent species status of Iris vorobievii N.S. Pavlova, Iris mandshurica Maxim., and Iris humilis Georgi (Iridaceae): Evidence from the nuclear and chloroplast genomes. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Tang S, Okashah RA, Cordonnier-Pratt MM, Pratt LH, Ed Johnson V, Taylor CA, Arnold ML, Knapp SJ. EST and EST-SSR marker resources for Iris. BMC PLANT BIOLOGY 2009; 9:72. [PMID: 19515254 PMCID: PMC2703627 DOI: 10.1186/1471-2229-9-72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 06/10/2009] [Indexed: 05/02/2023]
Abstract
BACKGROUND Limited DNA sequence and DNA marker resources have been developed for Iris (Iridaceae), a monocot genus of 200-300 species in the Asparagales, several of which are horticulturally important. We mined an I. brevicaulis-I. fulva EST database for simple sequence repeats (SSRs) and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications in Iris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database) and the cross-species utility and polymorphisms of I. brevicaulis-I. fulva EST-SSR markers among wild collected ecotypes and horticulturally important cultivars. RESULTS Collectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries of I. brevicaulis (IB72) and I. fulva (IF174), and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons). We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526) amplified alleles from IB72 and IF174 and 84% (335/399) were polymorphic between IB25 and IF174, the parents of I. brevicaulis x I. fulva mapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species - 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis, I.fulva, I. nelsonii, and I. hexagona), whereas 42-52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus, I. germanica, and I. sibirica). Ecotypes and cultivars were genetically diverse - the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76. CONCLUSION Nearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications in Iris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within the genus.
Collapse
Affiliation(s)
- Shunxue Tang
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Rebecca A Okashah
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602, USA
| | | | - Lee H Pratt
- Laboratory for Genomics and Bioinformatics, The University of Georgia, Athens, GA 30602, USA
| | - Virgil Ed Johnson
- Laboratory for Genomics and Bioinformatics, The University of Georgia, Athens, GA 30602, USA
| | - Christopher A Taylor
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Michael L Arnold
- Department of Genetics, The University of Georgia, Athens, GA 30602, USA
| | - Steven J Knapp
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
8
|
Kozyrenko MM, Artyukova EV, Boltenkov EV, Mironova LN, Zhuravlev YN. The species status of Iris vorobievii N.S. Pavlova, I. mandshurica Maxim., and I. humilis Georgi (Iridaceae): evidence from the plastid genome. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2009; 426:239-243. [PMID: 19650327 DOI: 10.1134/s0012496609030144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- M M Kozyrenko
- Institute of Biology and Soil Science, Far East Division, Russian Academy of Sciences, pr Stoletiya Vladivostoka 159, Vladivostok, 690022 Russia
| | | | | | | | | |
Collapse
|
9
|
Bonin A, Paris M, Després L, Tetreau G, David JP, Kilian A. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection. BMC Genomics 2008; 9:459. [PMID: 18837997 PMCID: PMC2579443 DOI: 10.1186/1471-2164-9-459] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 10/06/2008] [Indexed: 01/21/2023] Open
Abstract
Background For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT). One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito Aedes aegypti as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs) in the genome of this species. Results Ae. aegypti genomic representations were produced following a two-step procedure: (1) restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2) amplification of restriction fragments containing a particular MITE element called Pony using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the Pony element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished. Conclusion The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in Ae. egypti. Overall, our results testify of the flexibility of the DArT genotyping technique and open new prospects as regards its application to a wider range of species, including animals which have been refractory to it so far. DArT has also a role to play in the current burst of whole-genome scans carried out in various organisms, which track signatures of selection in order to unravel the basis of genetic adaptation.
Collapse
Affiliation(s)
- Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 09, France.
| | | | | | | | | | | |
Collapse
|
10
|
Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. Proc Natl Acad Sci U S A 2008; 105:13965-70. [PMID: 18772373 DOI: 10.1073/pnas.0804671105] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata. The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages.
Collapse
|
11
|
Cornman RS, Arnold ML. Characterization and comparative analysis of sequence-specific amplified polymorphisms based on two subfamilies of IRRE retrotransposons in Iris missouriensis (Iridaceae). Genetica 2008; 135:25-38. [PMID: 18297403 DOI: 10.1007/s10709-008-9248-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 02/12/2008] [Indexed: 10/22/2022]
Abstract
DNA markers based on transposable-element polymorphisms are potentially useful alternatives to anonymous fragment-length polymorphisms (AFLPs). We developed the retrotransposon sequence-specific amplified polymorphism (retrotransposon SSAP) technique for the angiosperm Iris missouriensis (Iridaceae) in order to evaluate its use in generating population-genetic markers. Our cloning strategy identified two groups of long-terminal repeat retrotransposons of the IRRE family. Primers homologous to conserved regions of these elements generated repeatable and polymorphic markers. In comparison, the AFLP protocol failed to produce useful markers in our hands in this species. To investigate the distribution and evolutionary tempo of the two retrotransposons, we developed a phylogeny of representative species of subgenus Limniris based on chloroplast sequence. Sequences of both groups of retrotransposons were widespread in Limniris, but we also found evidence of substantial sequence and copy-number evolution since the divergence of I. missouriensis from other Limniris species. We corroborated these results with quantitative real-time PCR estimates of relative copy number. Importantly, the geographic structure of retrotransposon SSAP was strikingly different for the two groups of retrotransposons, indicating that different mutational dynamics and/or selective pressures govern their distribution. Although these primers should be useful for population-genetic studies of Iris missouriensis and other Limniris species, our findings reinforce the need for caution in evaluating transposable-element markers used to analyze the relatedness of populations or cultivars, as very different conclusions may be reached depending on the sequence amplified.
Collapse
Affiliation(s)
- R Scott Cornman
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| | | |
Collapse
|