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Liu BB, Ren C, Kwak M, Hodel RGJ, Xu C, He J, Zhou WB, Huang CH, Ma H, Qian GZ, Hong DY, Wen J. Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere. J Integr Plant Biol 2022; 64:1020-1043. [PMID: 35274452 DOI: 10.1111/jipb.13246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
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Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Myounghai Kwak
- National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wen-Bin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, 27965, NC, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, 510D Mueller Laboratory, University Park, Pennsylvania, 16802, USA
| | - Guan-Ze Qian
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
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Yang Z, Ma W, He X, Zhao T, Yang X, Wang L, Ma Q, Liang L, Wang G. Species divergence and phylogeography of Corylus heterophylla Fisch complex (Betulaceae): Inferred from molecular, climatic and morphological data. Mol Phylogenet Evol 2022; 168:107413. [PMID: 35031460 DOI: 10.1016/j.ympev.2022.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 10/19/2022]
Abstract
Historical geo-climatic changes have shaped the geographical distributions and genetic diversity of numerous plant taxa in East Asia, which promote species divergence and ultimately speciation. Here, we integrated multiple approaches, including molecular phylogeography, ecological niche modeling, and morphological traits to examine the nucleotide diversity and interspecific divergence within Corylus heterophylla complex (C. heterophylla, C. kweichowensis, and C. yunnanensis). These three sibling taxa harbored similar high levels of nucleotide diversity at the species level. The molecular data (SCNG and cpDNA) unanimously supported the division of C. heterophylla complex into two major clades, with C. yunnanensis diverged earlier from the complex, whereas C. heterophylla and C. kweichowensis could hardly be separated. The split between the two clades (c. 12.89 Ma) coincided with the formation of Sichuan Basin in the middle Miocene, while the divergence among and within the five subclades (YUN1-YUN3, HK1-HK2) occurred from the late Miocene to the Pleistocene. C. heterophylla of northern China experienced glacial contraction and interglacial expansion during the Quaternary, whereas C. kweichowensis and C. yunnanensis of southern China presented population expansion even during the last glacial maximum. Despite of high levels of genetic admixture between C. heterophylla and C. kweichowensis, significant ecological and morphological discrepancy as well as incomplete geographic isolation indicated that adaptive evolution triggered by divergent selection may have played important roles in incipient ecological speciation.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Xin He
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
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Su N, Liu BB, Wang JR, Tong RC, Ren C, Chang ZY, Zhao L, Potter D, Wen J. On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology. Front Plant Sci 2021; 12:743643. [PMID: 34707629 PMCID: PMC8542774 DOI: 10.3389/fpls.2021.743643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 05/23/2023]
Abstract
The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Bin-bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
| | - Jun-ru Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Ru-chang Tong
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhao-yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, Davis, CA, United States
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
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Mao K, Ruhsam M, Ma Y, Graham SW, Liu J, Thomas P, Milne RI, Hollingsworth PM. A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae. Ann Bot 2019; 123:153-167. [PMID: 30124771 PMCID: PMC6344097 DOI: 10.1093/aob/mcy152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/21/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS Rapid evolutionary divergence and reticulate evolution may result in phylogenetic relationships that are difficult to resolve using small nucleotide sequence data sets. Next-generation sequencing methods can generate larger data sets that are better suited to solving these puzzles. One major and long-standing controversy in conifers concerns generic relationships within the subfamily Cupressoideae (105 species, approx. 1/6 of all conifers) of Cupressaceae, in particular the relationship between Juniperus, Cupressus and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) clade. Here we attempt to resolve this question using transcriptome-derived data. METHODS Transcriptome sequences of 20 species from Cupressoideae were collected. Using MarkerMiner, single-copy nuclear (SCN) genes were extracted. These were applied to estimate phylogenies based on concatenated data, species trees and a phylogenetic network. We further examined the effect of alternative backbone topologies on downstream analyses, including biogeographic inference and dating analysis. RESULTS Based on the 73 SCN genes (>200 000 bp total alignment length) we considered, all tree-building methods lent strong support for the relationship (HCX, (Juniperus, Cupressus)); however, strongly supported conflicts among individual gene trees were also detected. Molecular dating suggests that these three lineages shared a most recent common ancestor approx. 60 million years ago (Mya), and that Juniperus and Cupressus diverged about 56 Mya. Ancestral area reconstructions (AARs) suggest an Asian origin for the entire clade, with subsequent dispersal to North America, Europe and Africa. CONCLUSIONS Our analysis of SCN genes resolves a controversial phylogenetic relationship in the Cupressoideae, a major clade of conifers, and suggests that rapid evolutionary divergence and incomplete lineage sorting probably acted together as the source for conflicting phylogenetic inferences between gene trees and between our robust results and recently published studies. Our updated backbone topology has not substantially altered molecular dating estimates relative to previous studies; however, application of the latest AAR approaches has yielded a clearer picture of the biogeographic history of Cupressoideae.
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Affiliation(s)
- Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | | | - Yazhen Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | | | - Richard I Milne
- Institute of Molecular Plant Science, School of Biological Science, University of Edinburgh, Edinburgh, UK
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Latvis M, Jacobs SJ, Mortimer SME, Richards M, Blischak PD, Mathews S, Tank DC. Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci. Appl Plant Sci 2017; 5:apps.1700038. [PMID: 28989822 PMCID: PMC5628026 DOI: 10.3732/apps.1700038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/20/2017] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. METHODS AND RESULTS We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae. CONCLUSIONS These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae.
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Affiliation(s)
- Maribeth Latvis
- Department of Natural Resource Management, South Dakota State University, 1390 College Avenue, Brookings, South Dakota 57007 USA
| | - Sarah J. Jacobs
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, Idaho 83844-1133 USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
| | - Sebastian M. E. Mortimer
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, Idaho 83844-1133 USA
| | - Melissa Richards
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
| | - Paul D. Blischak
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 318 W. 12th Avenue, Columbus, Ohio 43210 USA
| | - Sarah Mathews
- Australian National Herbarium, CSIRO National Research Collections, Canberra, Australia
| | - David C. Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, Idaho 83844-1133 USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
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Latvis M, Jacobs SJ, Mortimer SME, Richards M, Blischak PD, Mathews S, Tank DC. Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci. Appl Plant Sci 2017. [PMID: 28989822 DOI: 10.5061/dryad.52v62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. METHODS AND RESULTS We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae. CONCLUSIONS These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae.
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Affiliation(s)
- Maribeth Latvis
- Department of Natural Resource Management, South Dakota State University, 1390 College Avenue, Brookings, South Dakota 57007 USA
| | - Sarah J Jacobs
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, Idaho 83844-1133 USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
| | - Sebastian M E Mortimer
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, Idaho 83844-1133 USA
| | - Melissa Richards
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
| | - Paul D Blischak
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 318 W. 12th Avenue, Columbus, Ohio 43210 USA
| | - Sarah Mathews
- Australian National Herbarium, CSIRO National Research Collections, Canberra, Australia
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, Idaho 83844-1133 USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051 USA
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Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Appl Plant Sci 2015; 3:apps1400115. [PMID: 25909041 PMCID: PMC4406834 DOI: 10.3732/apps.1400115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/25/2015] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. METHODS AND RESULTS We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. CONCLUSIONS MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.
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Affiliation(s)
- Srikar Chamala
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Author for correspondence:
| | - Nicolás García
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Grant T. Godden
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Rancho Santa Ana Botanic Garden, Claremont, California, USA
| | | | - Ingrid E. Jordon-Thaden
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
- Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA
| | - Riet De Smet
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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Ai B, Gao Y, Zhang X, Tao J, Kang M, Huang H. Comparative transcriptome resources of eleven Primulina species, a group of 'stone plants' from a biodiversity hot spot. Mol Ecol Resour 2014; 15:619-32. [PMID: 25243665 DOI: 10.1111/1755-0998.12333] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 11/28/2022]
Abstract
The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an N50 value of 2191 bp after pooling and reassembling twelve individual pre-assembled unigene sets. Of these unigenes, 249 973 (70%) were successfully annotated and 256 601 (72%) were identified as coding sequences (CDSs). We identified a total of 38 279 simple sequence repeats (SSRs) and 367 123 single nucleotide polymorphisms (SNPs). Marker validation assay revealed that 354 (27.3%) of the 1296 SSR and 795 (39.6%) of the 2008 SNP loci showed successful genotyping performance and exhibited expected polymorphism profiles. We screened 834 putative single-copy nuclear genes and proved their high effectiveness in phylogeny construction and estimation of ancestral population parameters. We identified a total of 85 candidate orthologs under positive selection for 46 of the 66 species pairs. This study provided an efficient application of RNA-seq in development of genomic resources for a group of 'stone plants' from south China Karst regions, a biodiversity hot spot of the World. The assembled unigenes with annotations and the massive gene-associated molecular markers would help guide further molecular systematic, population genetic and ecological genomics studies in Primulina and its relatives.
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Affiliation(s)
- Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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