1
|
Yolcu S, Skorupa M, Uras ME, Mazur J, Ozyiğit II. Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress. PLANTA 2024; 259:85. [PMID: 38448714 PMCID: PMC10917867 DOI: 10.1007/s00425-024-04361-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
MAIN CONCLUSION This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.
Collapse
Affiliation(s)
- Seher Yolcu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Türkiye.
| | - Monika Skorupa
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Mehmet Emin Uras
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Haliç University, 34060, Istanbul, Türkiye
| | - Justyna Mazur
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Ibrahim Ilker Ozyiğit
- Faculty of Science, Department of Biology, Marmara University, 34722, Istanbul, Türkiye
| |
Collapse
|
2
|
Zhou W, Shi W, Soltis PS, Soltis DE, Xiang QY(J. Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation. FRONTIERS IN PLANT SCIENCE 2023; 14:1274746. [PMID: 38192694 PMCID: PMC10773735 DOI: 10.3389/fpls.2023.1274746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024]
Abstract
Introduction The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America. Methods Metagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns. Results We found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus. However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed. Discussion Our results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus. The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species.
Collapse
Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Wei Shi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Qiu-Yun (Jenny) Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
3
|
Du ZY, Jenny Xiang QY, Cheng J, Zhou W, Wang QF, Soltis DE, Soltis PS. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data. AMERICAN JOURNAL OF BOTANY 2023; 110:e16116. [PMID: 36480351 DOI: 10.1002/ajb2.16116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
PREMISE A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. METHODS We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. RESULTS A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode. CONCLUSIONS Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.
Collapse
Affiliation(s)
- Zhi-Yuan Du
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jin Cheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
- Department of Biology, University of Florida, Gainesville, 32611 FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
| |
Collapse
|
4
|
Steenwyk JL, Goltz DC, Buida TJ, Li Y, Shen XX, Rokas A. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLoS Biol 2022; 20:e3001827. [PMID: 36228036 PMCID: PMC9595520 DOI: 10.1371/journal.pbio.3001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 10/25/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in 1 or more species-a phenomenon observed among several important families of genes such as transporters and transcription factors-are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure analogous to snapping branches on a tree. From 415,129 orthologous groups of genes inferred across 7 eukaryotic phylogenomic datasets, we identified 9,821 SC-OGs; using OrthoSNAP on the remaining 405,308 orthologous groups of genes, we identified an additional 10,704 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole-genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.
Collapse
Affiliation(s)
- Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (JLS); (AR)
| | - Dayna C. Goltz
- Independent Researcher, Nashville, Tennessee, United States of America
| | - Thomas J. Buida
- Independent Researcher, Nashville, Tennessee, United States of America
| | - Yuanning Li
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xing-Xing Shen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- * E-mail: (JLS); (AR)
| |
Collapse
|
5
|
Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022; 176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
|
6
|
He J, Lyu R, Luo Y, Xiao J, Xie L, Wen J, Li W, Pei L, Cheng J. A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae. Mol Phylogenet Evol 2022; 174:107545. [PMID: 35690374 DOI: 10.1016/j.ympev.2022.107545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]
Abstract
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using these data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.
Collapse
Affiliation(s)
- Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Wenhe Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Linying Pei
- Beijing Engineering Technology Research Center for Garden Plants, Beijing Forestry University Forest Science Co. Ltd., Beijing 100083, PR China
| | - Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| |
Collapse
|
7
|
Zhou W, Soghigian J, Xiang QYJ. A New Pipeline for Removing Paralogs in Target Enrichment Data. Syst Biol 2021; 71:410-425. [PMID: 34146111 PMCID: PMC8974407 DOI: 10.1093/sysbio/syab044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 06/04/2021] [Accepted: 06/12/2021] [Indexed: 12/30/2022] Open
Abstract
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing
method that has been increasingly used for phylogenomic studies. Unfortunately, current
widely used pipelines for analysis of target enrichment data do not have a vigorous
procedure to remove paralogs in target enrichment data. In this study, we develop a
pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs
from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and
the entire pipeline applies criteria in both sequence similarity and heterozygous sites at
each locus in the identification of paralogs. Users may adjust the thresholds of sequence
identity and heterozygous sites to identify and remove paralogs according to the level of
phylogenetic divergence of their group of interest. The new pipeline also removes highly
polymorphic sites attributed to errors in sequence assembly and gappy regions in the
alignment. We demonstrated the value of the new pipeline using empirical data generated
from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea
(Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales).
Comparisons of data sets showed that the PPD identified many more putative paralogs than
the popular method HybPiper. Comparisons of tree topologies and divergence times showed
evident differences between data from HybPiper and data from our new PPD pipeline. We
further evaluated the accuracy and error rates of PPD by BLAST mapping of putative
paralogous and orthologous sequences to a reference genome sequence of Castanea
mollissima. Compared to HybPiper alone, PPD identified substantially more
paralogous gene sequences that mapped to multiple regions of the reference genome (31
genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper,
paralogous genes identified by both pipelines can be removed resulting in the construction
of more robust orthologous gene data sets for phylogenomic and divergence time analyses.
Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353
probe set for elucidating species relationships within a genus, and argues for the
importance of additional steps to filter paralogous genes and poorly aligned regions
(e.g., as occur through assembly errors), such as our new PPD pipeline described in this
study. [Angiosperms353; Castanea; divergence time;
Hamamelis; Hyb-Seq, paralogs, phylogenomics.]
Collapse
Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27965, USA
| | - John Soghigian
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27965, USA
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27965, USA
| |
Collapse
|
8
|
Chen L, Lin Y, Xiao Q, Lin Y, Du Y, Lin C, Ward-Fear G, Hu C, Qu Y, Li H. Characterization of the complete mitochondrial genome of the many-lined sun skink (Eutropis multifasciata) and comparison with other Scincomorpha species. Genomics 2021; 113:2526-2536. [PMID: 34051326 DOI: 10.1016/j.ygeno.2021.05.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/04/2021] [Accepted: 05/25/2021] [Indexed: 11/28/2022]
Abstract
Characterizating the complete mitochondrial genome (mitogenome) of an organism allows detailed genomic studies in systematics and evolution. The present study decodes the mitogenome (17,062 bp) of the many-lined sun skink, Eutropis multifasciata, using next-generation sequencing. To compare the diversity of mitogenomic structure and investigate intraspecific evolutionary relationships among the Asian Scincomorpha, the mitogenomes of 46 other species were examined concurrently. Within the group, the size of mitogenomes varied predominantly in the length at their control regions. The Ka/Ks ratios of 12 protein codon genes (PCGs) were lower than 1.00, demonstrating that they were under relaxed or moderate purifying selection. However, the ND5 had a Ka/Ks ratio >1, and was considered to be under positive selection. Currently there are two superfamilies in Scincomorpha (i.e. Scincoidea and Lacertoidea), but phylogenetic analysis using Bayesian Inference and Maximum-Likelihood Estimations produced phylogenetic trees with three clades in Scincomorpha ((Scincoidea + Lacertoidea (part)) + Gymnophthalmidae)).
Collapse
Affiliation(s)
- Lian Chen
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Youfu Lin
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qi Xiao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying Lin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Hainan Key Laboratory for Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Chixian Lin
- Hainan Key Laboratory for Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Georgia Ward-Fear
- School of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yanfu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| |
Collapse
|
9
|
Melton AE, Chen S, Zhao Y, Fu C, Xiang QYJ, Cheng S, Wong GKS, Soltis PS, Soltis DE, Gitzendanner MA. Genetic insights into the evolution of genera with the eastern Asia-eastern North America floristic disjunction: a transcriptomics analysis. AMERICAN JOURNAL OF BOTANY 2020; 107:1736-1748. [PMID: 33280088 DOI: 10.1002/ajb2.1579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/29/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Large disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia-eastern North America (EA-ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly. METHODS To evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus. RESULTS No statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species-rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions. CONCLUSIONS Our data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.
Collapse
Affiliation(s)
- Anthony E Melton
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Shichao Chen
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunpeng Zhao
- Laboratory of Systematic and Evolutionary Botany & Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chengxin Fu
- Laboratory of Systematic and Evolutionary Botany & Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shifeng Cheng
- Beijing Genomics Institute, Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District, Shenzhen, China
| | - Gane K-S Wong
- Beijing Genomics Institute, Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District, Shenzhen, China
- Biological Sciences, The University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | | |
Collapse
|
10
|
Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous. Mol Phylogenet Evol 2020; 145:106726. [DOI: 10.1016/j.ympev.2019.106726] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 12/26/2019] [Accepted: 12/28/2019] [Indexed: 02/06/2023]
|
11
|
Coathup MJ, Osborne OG, Savolainen V. How predictable is genome evolution? eLife 2019; 8:50784. [PMID: 31517601 PMCID: PMC6744270 DOI: 10.7554/elife.50784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/24/2022] Open
Abstract
Similar patterns of genomic divergence have been observed in the evolution of plant species separated by oceans.
Collapse
Affiliation(s)
- Matthew J Coathup
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Owen G Osborne
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| |
Collapse
|
12
|
Dong Y, Chen S, Cheng S, Zhou W, Ma Q, Chen Z, Fu CX, Liu X, Zhao YP, Soltis PS, Wong GKS, Soltis DE, Xiang QYJ. Natural selection and repeated patterns of molecular evolution following allopatric divergence. eLife 2019; 8:45199. [PMID: 31373555 PMCID: PMC6744222 DOI: 10.7554/elife.45199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/01/2019] [Indexed: 11/13/2022] Open
Abstract
Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10-15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.
Collapse
Affiliation(s)
- Yibo Dong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States.,Plant Biology Division, Noble Research Institute, Ardmore, United States
| | - Shichao Chen
- Florida Museum of Natural History, University of Florida, Gainesville, United States.,Department of Biology, University of Florida, Gainesville, United States.,School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Qing Ma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Xin Fu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xin Liu
- Beijing Genomics Institute, Shenzhen, China
| | - Yun-Peng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, United States
| | - Gane Ka-Shu Wong
- Beijing Genomics Institute, Shenzhen, China.,Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Medicine, University of Alberta, Edmonton, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, United States.,Department of Biology, University of Florida, Gainesville, United States
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| |
Collapse
|