1
|
Holt SD, Sigel EM, Sutherland BL, Schwartsburd PB, Beck JB. What is Salvinia molesta (Salviniaceae)? Determining the maternal progenitor and genetic diversity of the clonal invasive fern giant salvinia. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03028-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
2
|
Brock JR, Mandáková T, McKain M, Lysak MA, Olsen KM. Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa. HORTICULTURE RESEARCH 2022; 9:uhab050. [PMID: 35031794 PMCID: PMC8788360 DOI: 10.1093/hr/uhab050] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 05/24/2023]
Abstract
The genus Camelina (Brassicaceae) comprises 7-8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.
Collapse
Affiliation(s)
- Jordan R Brock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130 USA
| | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michael McKain
- Department of Biological Sciences, The University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, Alabama, 35487 USA
| | - Martin A Lysak
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130 USA
| |
Collapse
|
3
|
Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. Front Genet 2020; 10:1407. [PMID: 32153629 PMCID: PMC7047930 DOI: 10.3389/fgene.2019.01407] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
Collapse
Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Maria Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Romina Batista
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv–Instituto Nacional de Pesquisas da Amazônia—INPA Campus II, Manaus, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - José L. Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Isabel M. Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond-Surrey, United Kingdom
| |
Collapse
|
4
|
McAllister CA, McKain MR, Li M, Bookout B, Kellogg EA. Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0403. [PMID: 30455217 DOI: 10.1098/rstb.2017.0403] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 01/10/2023] Open
Abstract
Herbaria contain a cumulative sample of the world's flora, assembled by thousands of people over centuries. To capitalize on this resource, we conducted a specimen-based analysis of a major clade in the grass tribe Andropogoneae, including the dominant species of the world's grasslands in the genera Andropogon, Schizachyrium, Hyparrhenia and several others. We imaged 186 of the 250 named species of the clade, georeferenced the specimens and extracted climatic variables for each. Using semi- and fully automated image analysis techniques, we extracted spikelet morphological characters and correlated these with environmental variables. We generated chloroplast genome sequences to correct for phylogenetic covariance and here present a new phylogeny for 81 of the species. We confirm and extend earlier studies to show that Andropogon and Schizachyrium are not monophyletic. In addition, we find all morphological and ecological characters are homoplasious but variable among clades. For example, sessile spikelet length is positively correlated with awn length when all accessions are considered, but when separated by clade, the relationship is positive for three sub-clades and negative for three others. Climate variables showed no correlation with morphological variation in the spikelet pair; only very weak effects of temperature and precipitation were detected on macrohair density.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Collapse
Affiliation(s)
| | - Michael R McKain
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA.,Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Mao Li
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA
| | - Bess Bookout
- Department of Biology and Natural Resources, Principia College, Elsah, IL, USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA
| |
Collapse
|
5
|
McKain MR, Johnson MG, Uribe‐Convers S, Eaton D, Yang Y. Practical considerations for plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1038. [PMID: 29732268 PMCID: PMC5895195 DOI: 10.1002/aps3.1038] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/13/2018] [Indexed: 05/10/2023]
Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project-dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-and-coming technologies that may help propel the field even further.
Collapse
Affiliation(s)
- Michael R. McKain
- Department of Biological SciencesThe University of AlabamaBox 870344TuscaloosaAlabama35487USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main Street, Box 43131LubbockTexas79409USA
| | - Simon Uribe‐Convers
- Department of Ecology and Evolutionary BiologyUniversity of Michigan830 North UniversityAnn ArborMichigan48109USA
| | - Deren Eaton
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam AvenueNew YorkNew York10027USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota–Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108USA
| |
Collapse
|