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Liu S, Wu Z, Yang T, Xu J, Aishan S, Qin E, Ma K, Liu J, Qin R, Wang J, Tie J, Liu H. The Chrysosplenium sinicum genome provides insights into adaptive evolution of shade plants. Commun Biol 2024; 7:1004. [PMID: 39152309 PMCID: PMC11329650 DOI: 10.1038/s42003-024-06701-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024] Open
Abstract
Chrysosplenium sinicum, a traditional Tibetan medicinal plant, can successfully thrive in low-light environments for long periods of time. To investigate the adaptive evolution of shade plants in low-light environments, we generated a chromosome-scale genome assembly (~320 Mb) for C. sinicum by combining PacBio sequencing and Hi-C technologies. Based on our results, gene families related to photosynthesis and cell respiration greatly expanded and evolved in C. sinicum genome due to intracellular DNA transfer from organelle genome to nuclear genome. Under positive selective pressure, adaptive evolution of light-harvesting complex II (LHCII) component protein CsLhcb1s resulted in the expansion of threonine residues at the phosphorylation site of STN7 kinase, potentially establishing a crucial genomic foundation for enhancing C. sinicum's adaptability in low-light environments. Through transcriptome and metabolome analysis, we identified chrysosplenol and chrysosplenoside as predominant flavonoid metabolites of C. sinicum and predicted their synthesis pathways. In addition, analysis of alternative splicing (AS) revealed that AS events help regulate state transition and flavonoid biosynthesis. The present study provides new insights into the genomes of shade plants exposed to low-light conditions and adaptive evolution of these genomes; in addition, the results improve our current knowledge on the biosynthetic and regulatory processes of chrysosplenol and chrysosplenoside.
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Affiliation(s)
- Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Saimire Aishan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Erdai Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Kang Ma
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jiangqing Wang
- College of Computer Science, South-Central Minzu University, Wuhan, China
| | - Jun Tie
- College of Computer Science, South-Central Minzu University, Wuhan, China.
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China.
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Zhao H, Qin L, Deng X, Wang Z, Jiang R, Reitz SR, Wu S, He Z. Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105608. [PMID: 38796047 DOI: 10.1016/j.meegid.2024.105608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.
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Affiliation(s)
- Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Stuart R Reitz
- Malheur Experiment Station, Oregon State University, Ontario, OR, USA
| | - Shengyong Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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Johnston SE. Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future. Mol Biol Evol 2024; 41:msae112. [PMID: 38959451 PMCID: PMC11221659 DOI: 10.1093/molbev/msae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/05/2024] Open
Abstract
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms of recombination are remarkably conserved across eukaryotes, yet meiotic genes and proteins show substantial variation in their sequence and function, even between closely related species. Furthermore, the rate and distribution of recombination shows a huge diversity within and between chromosomes, individuals, sexes, populations, and species. This variation has implications for many molecular and evolutionary processes, yet how and why this diversity has evolved is not well understood. A key step in understanding trait evolution is to determine its genetic basis-that is, the number, effect sizes, and distribution of loci underpinning variation. In this perspective, I discuss past and current knowledge on the genetic basis of variation in recombination rate and distribution, explore its evolutionary implications, and present open questions for future research.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Phillips AR. Variant calling in polyploids for population and quantitative genetics. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11607. [PMID: 39184203 PMCID: PMC11342233 DOI: 10.1002/aps3.11607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/03/2024] [Accepted: 04/10/2024] [Indexed: 08/27/2024]
Abstract
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
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Affiliation(s)
- Alyssa R. Phillips
- Department of Evolution and EcologyUniversity of California, DavisDavis95616CaliforniaUSA
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Toll K, Willis JH. The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers. Evolution 2024; 78:111-126. [PMID: 37930045 DOI: 10.1093/evolut/qpad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/17/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the Mimulus guttatus species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, M. nudatus, and its close relative M. guttatus. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral, and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together, our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives.
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Affiliation(s)
- Katherine Toll
- Department of Biology, Duke University, Durham, NC, United States
| | - John H Willis
- Department of Biology, Duke University, Durham, NC, United States
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Kumawat S, Martinez I, Logeswaran D, Chen H, Coughlan JM, Chen JJL, Yuan Y, Sobel JM, Choi JY. Transposition, duplication, and divergence of the telomerase RNA underlies the evolution of Mimulus telomeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.568249. [PMID: 38106000 PMCID: PMC10723376 DOI: 10.1101/2023.12.06.568249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Telomeres are nucleoprotein complexes with a crucial role of protecting chromosome ends. It consists of simple repeat sequences and dedicated telomere-binding proteins. Because of its vital functions, components of the telomere, for example its sequence, should be under strong evolutionary constraint. But across all plants, telomere sequences display a range of variation and the evolutionary mechanism driving this diversification is largely unknown. Here, we discovered in Monkeyflower (Mimulus) the telomere sequence is even variable between species. We investigated the basis of Mimulus telomere sequence evolution by studying the long noncoding telomerase RNA (TR), which is a core component of the telomere maintenance complex and determines the telomere sequence. We conducted total RNA-based de novo transcriptomics from 16 Mimulus species and analyzed reference genomes from 6 species, and discovered Mimulus species have evolved at least three different telomere sequences: (AAACCCT)n, (AAACCCG)n, and (AAACCG)n. Unexpectedly, we discovered several species with TR duplications and the paralogs had functional consequences that could influence telomere evolution. For instance, M. lewisii had two sequence-divergent TR paralogs and synthesized a telomere with sequence heterogeneity, consisting of AAACCG and AAACCCG repeats. Evolutionary analysis of the M. lewisii TR paralogs indicated it had arisen from a transposition-mediate duplication process. Further analysis of the TR from multiple Mimulus species showed the gene had frequently transposed and inserted into new chromosomal positions during Mimulus evolution. From our results, we propose the TR transposition, duplication, and divergence model to explain the evolutionary sequence turnovers in Mimulus and potentially all plant telomeres.
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Affiliation(s)
- Surbhi Kumawat
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Irene Martinez
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, New York, USA
| | | | - Hongfei Chen
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Jenn M. Coughlan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | | | - Yaowu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - James M. Sobel
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, New York, USA
| | - Jae Young Choi
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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Wu X, Simpson SA, Youngblood RC, Liu XF, Scheffler BE, Rinehart TA, Alexander LW, Hulse-Kemp AM. Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea ( Hydrangea macrophylla) and insights into Asterid evolution. HORTICULTURE RESEARCH 2023; 10:uhad217. [PMID: 38130599 PMCID: PMC10734616 DOI: 10.1093/hr/uhad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 12/23/2023]
Abstract
The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.
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Affiliation(s)
- Xingbo Wu
- Department of Environmental Horticulture, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, United States
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, United States
| | - Xiaofen F Liu
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Timothy A Rinehart
- Crop Production and Protection, USDA-ARS, Beltsville, MD 20705, United States
| | - Lisa W Alexander
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, USDA-ARS, McMinnville, TN 37110, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, United States
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White OW, Reyes-Betancort A, Carine MA, Chapman MA. Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum. G3 (BETHESDA, MD.) 2023; 13:jkad158. [PMID: 37477910 PMCID: PMC10542503 DOI: 10.1093/g3journal/jkad158] [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: 04/21/2023] [Revised: 04/21/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023]
Abstract
Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.
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Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Feng X, Li G, Wu W, Lyu H, Wang J, Liu C, Zhong C, Shi S, He Z. Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:155-168. [PMID: 37275537 PMCID: PMC10232687 DOI: 10.1007/s42995-023-00177-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
Mangroves are adapted to intertidal zones, which present extreme environmental conditions. WRKYs are among the most prominent transcription factors (TFs) in higher plants and act through various interconnected networks to regulate responses to multiple abiotic stressors. Here, based on omic data, we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus Avicennia. We found that both the number and the proportion of TFs and WRKYs in Avicennia species exceeded their inland relatives, indicating a significant expansion of WRKYs in Avicennia. We identified 109 WRKY genes in the representative species Avicennia marina. Comparative genomic analysis showed that two recent whole-genome duplication (WGD) events played a critical role in the expansion of WRKYs, and 88% of Avicennia marina WRKYs (AmWRKYs) have been retained following these WGDs. Applying comparative transcriptomics on roots under experimental salt gradients, we inferred that there is high divergence in the expression of WGD-retained AmWRKYs. Moreover, we found that the expression of 16 AmWRKYs was stable between freshwater and moderately saline water but increased when the trees were exposed to high salinity. In particular, 14 duplicates were retained following the two recent WGD events, indicating potential neo- and sub-functionalization. We also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance, contributing to the adaptation to intertidal zones. Our omic data of the WRKY family in A. marina broadens the understanding of how a TF family relates to the adaptive evolution of mangroves. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00177-y.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458 China
| | - Guohong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Weihong Wu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Haomin Lyu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Cong Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100 China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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Liang M, Chen W, LaFountain AM, Liu Y, Peng F, Xia R, Bradshaw H, Yuan YW. Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers. Science 2023; 379:576-582. [PMID: 36758083 PMCID: PMC10601778 DOI: 10.1126/science.adf1323] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/06/2022] [Indexed: 02/11/2023]
Abstract
Taxon-specific small RNA loci are widespread in eukaryotic genomes, yet their role in lineage-specific adaptation, phenotypic diversification, and speciation is poorly understood. Here, we report that a speciation locus in monkeyflowers (Mimulus), YELLOW UPPER (YUP), contains an inverted repeat region that produces small interfering RNAs (siRNAs) in a phased pattern. Although the inverted repeat is derived from a partial duplication of a protein-coding gene that is not involved in flower pigmentation, one of the siRNAs targets and represses a master regulator of floral carotenoid pigmentation. YUP emerged with two protein-coding genes that control other aspects of flower coloration as a "superlocus" in a subclade of Mimulus and has contributed to subsequent phenotypic diversification and pollinator-mediated speciation in the descendant species.
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Affiliation(s)
- Mei Liang
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Wenjie Chen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding and Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
| | - Amy M. LaFountain
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Foen Peng
- Department of Biology, University of Washington, Seattle, WA 98195
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - H.D. Bradshaw
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
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Wang M, Huang J, Liu S, Liu X, Li R, Luo J, Fu Z. Improved assembly and annotation of the sesame genome. DNA Res 2022; 29:6821245. [PMID: 36355766 PMCID: PMC9724774 DOI: 10.1093/dnares/dsac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an important oilseed crop that produces abundant seed oil and has a pleasant flavor and high nutritional value. To date, several Illumina-based genome assemblies corresponding to different sesame genotypes have been published and widely used in genetic and genomic studies of sesame. However, these assemblies consistently showed low continuity with numerous gaps. Here, we reported a high-quality, reference-level sesame genome assembly by integrating PacBio high-fidelity sequencing and Hi-C technology. Our updated sesame assembly was 309.35 Mb in size with a high chromosome anchoring rate (97.54%) and contig N50 size (13.48 Mb), which were better than previously published genomes. We identified 163.38 Mb repetitive elements and 24,345 high-confidence protein-coding genes in the updated sesame assembly. Comparative genomic analysis showed that sesame shared an ancient whole-genome duplication event with two Lamiales species. A total of 2,782 genes were tandemly duplicated. We also identified several genes that were likely involved in fatty acid and triacylglycerol biosynthesis. Our improved sesame assembly and annotation will facilitate future genetic studies and genomics-assisted breeding of sesame.
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Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, No. 2025 Chengluo Road, Chengdu 610106, China,Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, Chengdu 610106, China
| | | | - Song Liu
- Berry Genomics Corporation, Beijing 100015, China
| | - Xiaofeng Liu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, Chengdu 610106, China,School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Junjia Luo
- To whom correspondence should be addressed. (J.L.); (Z.F.)
| | - Zhixi Fu
- To whom correspondence should be addressed. (J.L.); (Z.F.)
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Hou Q, Zhang T, Qi Y, Dong Z, Wan X. Epigenetic Dynamics and Regulation of Plant Male Reproduction. Int J Mol Sci 2022; 23:ijms231810420. [PMID: 36142333 PMCID: PMC9499625 DOI: 10.3390/ijms231810420] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Flowering plant male germlines develop within anthers and undergo epigenetic reprogramming with dynamic changes in DNA methylation, chromatin modifications, and small RNAs. Profiling the epigenetic status using different technologies has substantially accumulated information on specific types of cells at different stages of male reproduction. Many epigenetically related genes involved in plant gametophyte development have been identified, and the mutation of these genes often leads to male sterility. Here, we review the recent progress on dynamic epigenetic changes during pollen mother cell differentiation, microsporogenesis, microgametogenesis, and tapetal cell development. The reported epigenetic variations between male fertile and sterile lines are summarized. We also summarize the epigenetic regulation-associated male sterility genes and discuss how epigenetic mechanisms in plant male reproduction can be further revealed.
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14
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Smith RD, Puzey JR, Conradi Smith GD. Population genetics of transposable element load: A mechanistic account of observed overdispersion. PLoS One 2022; 17:e0270839. [PMID: 35834543 PMCID: PMC9282655 DOI: 10.1371/journal.pone.0270839] [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: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
In an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 300). To obtain insight regarding the evolutionary genetic mechanisms that underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analyses of population distributions of TE load reveal that overdispersion is likely to arise via copy-and-paste proliferation dynamics, especially when the elementary processes of proliferation and excision are approximately balanced. Parameter studies and analytic work confirm this result and further suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.
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Affiliation(s)
- Ronald D. Smith
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
| | - Joshua R. Puzey
- Department of Biology, William & Mary, Williamsburg, VA, United States of America
| | - Gregory D. Conradi Smith
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
- * E-mail:
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15
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Morales‐Briones DF, Lin N, Huang EY, Grossenbacher DL, Sobel JM, Gilmore CD, Tank DC, Yang Y. Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades. AMERICAN JOURNAL OF BOTANY 2022; 109:1035-1046. [PMID: 35462411 PMCID: PMC9328367 DOI: 10.1002/ajb2.1860] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons. METHODS We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and a cloudogram, and carried out reticulation analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distances, and gene duplication events as evidence. RESULTS Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, the monophyly of Mimulus s.l. is rejected, and no individual reticulation event among the Phrymaceae tribes is well-supported. Reticulation likely occurred among Erythranthe bicolor and closely related species. No ancient WGD was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. CONCLUSIONS We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that phylogenomic datasets using genomes and transcriptomes present rich opportunities to investigate gene family evolution and genome duplication events involved in lineage diversification and adaptation.
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Affiliation(s)
- Diego F. Morales‐Briones
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig‐Maximilians‐Universität MünchenMenzinger Strasse 6780638MunichGermany
| | - Nan Lin
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- College of Life ScienceHenan Agricultural University63 Nongye RoadZhengzhouHenan450002China
| | - Eileen Y. Huang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
| | - Dena L. Grossenbacher
- Biological Sciences DepartmentCalifornia Polytechnic State University, 1 Grand Avenue, San Luis ObispoCalifornia93407USA
| | - James M. Sobel
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - Caroline D. Gilmore
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - David C. Tank
- Department of Botany & Rocky Mountain HerbariumUniversity of Wyoming, 1000 E. University Avenue, LaramieWyoming82071USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
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16
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Genome-Wide Prediction of Transcription Start Sites in Conifers. Int J Mol Sci 2022; 23:ijms23031735. [PMID: 35163661 PMCID: PMC8836283 DOI: 10.3390/ijms23031735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 02/04/2023] Open
Abstract
The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms.
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17
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Brown KE, Kelly JK. Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations. Genetics 2022; 220:iyab189. [PMID: 34791192 PMCID: PMC8733635 DOI: 10.1093/genetics/iyab189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the allele frequency spectrum of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with "rarity disequilibrium" produce a superabundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of coexpressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high "connectedness" (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.
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Affiliation(s)
- Keely E Brown
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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18
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PRDM9-directed recombination hotspots depleted near meiotically transcribed genes. Gene 2021; 813:146123. [PMID: 34952174 DOI: 10.1016/j.gene.2021.146123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/22/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022]
Abstract
PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.
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19
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Huff M, Seaman J, Wu D, Zhebentyayeva T, Kelly LJ, Faridi N, Nelson CD, Cooper E, Best T, Steiner K, Koch J, Romero Severson J, Carlson JE, Buggs R, Staton M. A high quality reference genome for Fraxinus pennsylvanica for ash species restoration and research. Mol Ecol Resour 2021; 22:1284-1302. [PMID: 34748273 PMCID: PMC9299157 DOI: 10.1111/1755-0998.13545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]
Abstract
Green ash (Fraxinus pennsylvanica) is the most widely distributed ash tree in North America. Once common, it has experienced high mortality from the non‐native invasive emerald ash borer (EAB; Agrilus planipennis). A small percentage of native green ash trees that remain healthy in long‐infested areas, termed “lingering ash,” display partial resistance to the insect, indicating that breeding and propagating populations with higher resistance to EAB may be possible. To assist in ash breeding, ecology and evolution studies, we report the first chromosome‐level assembly from the genus Fraxinus for F. pennsylvanica with over 99% of bases anchored to 23 haploid chromosomes, spanning 757 Mb in total, composed of 49.43% repetitive DNA, and containing 35,470 high‐confidence gene models assigned to 22,976 Asterid orthogroups. We also present results of range‐wide genetic variation studies, the identification of candidate genes for important traits including potential EAB‐resistance genes, and an investigation of comparative genome organization among Asterids based on this reference genome platform. Residual duplicated regions within the genome probably resulting from a recent whole genome duplication event in Oleaceae were visualized in relation to wild olive (Olea europaea var. sylvestris). We used our F. pennsylvanica chromosome assembly to construct reference‐guided assemblies of 27 previously sequenced Fraxinus taxa, including F. excelsior. Thus, we present a significant step forward in genomic resources for research and protection of Fraxinus species.
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Affiliation(s)
- Matt Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Josiah Seaman
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Di Wu
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nurul Faridi
- USDA Forest Service, Southern Research Station, Saucier, Mississippi, USA.,Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas, USA
| | - Charles Dana Nelson
- USDA Forest Service, Southern Research Station, Saucier, Mississippi, USA.,Forest Health Research and Education Center, University of Kentucky, Lexington, Kentucky, USA
| | - Endymion Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Teodora Best
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kim Steiner
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jennifer Koch
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, Ohio, USA
| | - Jeanne Romero Severson
- Department of Biological Sciences, Notre Dame University, 46556, Notre Dame, Indiana, USA
| | - John E Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Richard Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
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20
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Cao Y, Sun G, Zhai X, Xu P, Ma L, Deng M, Zhao Z, Yang H, Dong Y, Shang Z, Lv Y, Yan L, Liu H, Cao X, Li B, Wang Z, Zhao X, Yu H, Wang F, Ma W, Huang J, Fan G. Genomic insights into the fast growth of paulownias and the formation of Paulownia witches' broom. MOLECULAR PLANT 2021; 14:1668-1682. [PMID: 34214658 DOI: 10.1016/j.molp.2021.06.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Paulownias are among the fastest growing trees in the world, but they often suffer tremendous loss of wood production due to infection by Paulownia witches' broom (PaWB) phytoplasmas. In this study, we have sequenced and assembled a high-quality nuclear genome of Paulownia fortunei, a commonly cultivated paulownia species. The assembled genome of P. fortunei is 511.6 Mb in size, with 93.2% of its sequences anchored to 20 pseudo-chromosomes, and it contains 31 985 protein-coding genes. Phylogenomic analyses show that the family Paulowniaceae is sister to a clade composed of Phrymaceae and Orobanchaceae. Higher photosynthetic efficiency is achieved by integrating C3 photosynthesis and the crassulacean acid metabolism pathway, which may contribute to the extremely fast growth habit of paulownia trees. Comparative transcriptome analyses reveal modules related to cambial growth and development, photosynthesis, and defense responses. Additional genome sequencing of PaWB phytoplasma, combined with functional analyses, indicates that the effector PaWB-SAP54 interacts directly with Paulownia PfSPLa, which in turn causes the degradation of PfSPLa by the ubiquitin-mediated pathway and leads to the formation of witches' broom. Taken together, these results provide significant insights into the biology of paulownias and the regulatory mechanism for the formation of PaWB.
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Affiliation(s)
- Yabing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Guiling Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Xiaoqiao Zhai
- Henan Academy of Forestry, Zhengzhou, Henan 450002, China
| | - Pingluo Xu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Liming Ma
- Biomarker Technologies Corporation, Beijing 101399, China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Haibo Yang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhonghai Shang
- Henan Academy of Forestry, Zhengzhou, Henan 450002, China
| | - Yujie Lv
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Lijun Yan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Haifang Liu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xibing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Bingbing Li
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhe Wang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xiaogai Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101399, China
| | - Fan Wang
- Biomarker Technologies Corporation, Beijing 101399, China
| | - Wen Ma
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Jinling Huang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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21
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Gutiérrez Pinzón Y, González Kise JK, Rueda P, Ronceret A. The Formation of Bivalents and the Control of Plant Meiotic Recombination. FRONTIERS IN PLANT SCIENCE 2021; 12:717423. [PMID: 34557215 PMCID: PMC8453087 DOI: 10.3389/fpls.2021.717423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/13/2021] [Indexed: 06/06/2023]
Abstract
During the first meiotic division, the segregation of homologous chromosomes depends on the physical association of the recombined homologous DNA molecules. The physical tension due to the sites of crossing-overs (COs) is essential for the meiotic spindle to segregate the connected homologous chromosomes to the opposite poles of the cell. This equilibrated partition of homologous chromosomes allows the first meiotic reductional division. Thus, the segregation of homologous chromosomes is dependent on their recombination. In this review, we will detail the recent advances in the knowledge of the mechanisms of recombination and bivalent formation in plants. In plants, the absence of meiotic checkpoints allows observation of subsequent meiotic events in absence of meiotic recombination or defective meiotic chromosomal axis formation such as univalent formation instead of bivalents. Recent discoveries, mainly made in Arabidopsis, rice, and maize, have highlighted the link between the machinery of double-strand break (DSB) formation and elements of the chromosomal axis. We will also discuss the implications of what we know about the mechanisms regulating the number and spacing of COs (obligate CO, CO homeostasis, and interference) in model and crop plants.
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22
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Feng X, Li G, Xu S, Wu W, Chen Q, Shao S, Liu M, Wang N, Zhong C, He Z, Shi S. Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum. THE NEW PHYTOLOGIST 2021; 231:2346-2358. [PMID: 34115401 DOI: 10.1111/nph.17551] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/02/2021] [Indexed: 06/12/2023]
Abstract
Mangroves have colonised extreme intertidal environments characterised by high salinity, hypoxia and other abiotic stresses. Aegiceras corniculatum, a pioneer mangrove species that has evolved two specialised adaptive traits (salt secretion and crypto-vivipary) is an attractive ecological model to investigate molecular mechanisms underlying adaptation to intertidal environments. We assembled de novo a high-quality reference genome of A. corniculatum and performed comparative genomic and transcriptomic analyses to investigate molecular mechanisms underlying adaptation to intertidal environments. We provide evidence that A. corniculatum experienced a whole-genome duplication (WGD) event c. 35 Ma. We infer that maintenance of cellular environmental homeostasis is an important adaptive process in A. corniculatum. The 14-3-3 and H+ -ATPase protein-coding genes, essential for the salt homeostasis, were preferentially retained after the recent WGD event. Using comparative transcriptomics, we show that genes upregulated under high-salt conditions are involved in salt transport and ROS scavenging. We also found that all homologues of DELAY OF GERMINATION1 (DOG1) had lost their heme-binding ability in A. corniculatum, and that this may contribute to crypto-vivipary. Our study provides insight into the genomic correlates of phenotypic adaptation to intertidal environments. This could contribute not only within the genomics community, but also to the field of plant evolution.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guohong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Min Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nan Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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23
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Jia KH, Liu H, Zhang RG, Xu J, Zhou SS, Jiao SQ, Yan XM, Tian XC, Shi TL, Luo H, Li ZC, Bao YT, Nie S, Guo JF, Porth I, El-Kassaby YA, Wang XR, Chen C, Van de Peer Y, Zhao W, Mao JF. Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. HORTICULTURE RESEARCH 2021; 8:177. [PMID: 34465761 PMCID: PMC8408255 DOI: 10.1038/s41438-021-00614-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 05/11/2023]
Abstract
Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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Affiliation(s)
- Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, 261000, Shandong, China
| | - Jie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Mei Yan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Chan Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hang Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhi-Chao Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Tao Bao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing-Fang Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xiao-Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden.
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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24
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Kinser TJ, Smith RD, Lawrence AH, Cooley AM, Vallejo-Marín M, Conradi Smith GD, Puzey JR. Endosperm-based incompatibilities in hybrid monkeyflowers. THE PLANT CELL 2021; 33:2235-2257. [PMID: 33895820 PMCID: PMC8364248 DOI: 10.1093/plcell/koab117] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/15/2021] [Indexed: 05/31/2023]
Abstract
Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.
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Affiliation(s)
- Taliesin J. Kinser
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| | - Ronald D. Smith
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185
| | - Amelia H. Lawrence
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| | | | - Mario Vallejo-Marín
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland FK9 4LA, UK
| | | | - Joshua R. Puzey
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
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25
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Colicchio JM, Hamm LN, Verdonk HE, Kooyers NJ, Blackman BK. Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome. Mol Ecol 2021; 30:6486-6507. [PMID: 34289200 DOI: 10.1111/mec.16087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome-wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population-level, whole genome resequencing data obtained from annual Mimulus guttatus individuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among-population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype-environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.
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Affiliation(s)
- Jack M Colicchio
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Lauren N Hamm
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Hannah E Verdonk
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nicholas J Kooyers
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Louisiana, Lafayette, Lafayette, Louisiana, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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26
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Milosavljevic S, Kuo T, Decarli S, Mohn L, Sese J, Shimizu KK, Shimizu-Inatsugi R, Robinson MD. ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics 2021; 22:547. [PMID: 34273949 PMCID: PMC8285871 DOI: 10.1186/s12864-021-07845-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid's parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. RESULTS We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC's performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO's output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. CONCLUSIONS The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO .
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Affiliation(s)
- Stefan Milosavljevic
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Tony Kuo
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Samuele Decarli
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Lucas Mohn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jun Sese
- AIST Artificial Intelligence Research Center, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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27
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Liu L, Li J, Wen J, He Y. Genome-wide analyses of tandem repeats and transposable elements in patchouli. Genes Genet Syst 2021; 96:81-87. [PMID: 33883323 DOI: 10.1266/ggs.20-00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Patchouli, Pogostemon cablin (Blanco) Benth., is a traditional Chinese medicinal plant from the order Lamiales. It is considered a valuable herb due to its essential oil content and range of therapeutic effects. This study aimed to explore the evolutionary history of repetitive sequences in the patchouli genome by analyzing tandem repeats and transposable elements (TEs). We first retrieved genomic data for patchouli and four other Lamiales species from the GenBank database. Next, the content of tandem repeats with different period sizes was identified. Long terminal repeats (LTRs) were then identified with LTR_STRUC. Finally, the evolutionary landscape of TEs was explored using an in-house PERL program. The analysis of repetitive sequences revealed that tandem repeats constitute a higher proportion of the patchouli genome compared to the four other species. Analyses of TE families showed that most of the repetitive sequences in the patchouli genome are TEs, and that recently inserted TEs make up a comparatively larger proportion than older ones. Our analyses of LTR retrotransposons in their host genome indicated the existence of ancient LTR retrotransposon expansion, and the escape of these elements from natural selection revealed their ages. Our identification and analyses of repetitive sequences should provide new insights for further investigation of patchouli evolution.
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Affiliation(s)
- Linqiu Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine
| | - Junjun Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine
| | - Jiawei Wen
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine
| | - Yang He
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine
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28
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Hasan AR, Ness RW. Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii. Genome Biol Evol 2021; 12:370-380. [PMID: 32181819 PMCID: PMC7186780 DOI: 10.1093/gbe/evaa057] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
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29
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Sandler G, Wright SI, Agrawal AF. Patterns and Causes of Signed Linkage Disequilibria in Flies and Plants. Mol Biol Evol 2021; 38:4310-4321. [PMID: 34097067 PMCID: PMC8476167 DOI: 10.1093/molbev/msab169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most empirical studies of linkage disequilibrium (LD) study its magnitude, ignoring its sign. Here, we examine patterns of signed LD in two population genomic data sets, one from Capsella grandiflora and one from Drosophila melanogaster. We consider how processes such as drift, admixture, Hill–Robertson interference, and epistasis may contribute to these patterns. We report that most types of mutations exhibit positive LD, particularly, if they are predicted to be less deleterious. We show with simulations that this pattern arises easily in a model of admixture or distance-biased mating, and that genome-wide differences across site types are generally expected due to differences in the strength of purifying selection even in the absence of epistasis. We further explore how signed LD decays on a finer scale, showing that loss of function mutations exhibit particularly positive LD across short distances, a pattern consistent with intragenic antagonistic epistasis. Controlling for genomic distance, signed LD in C. grandiflora decays faster within genes, compared with between genes, likely a by-product of frequent recombination in gene promoters known to occur in plant genomes. Finally, we use information from published biological networks to explore whether there is evidence for negative synergistic epistasis between interacting radical missense mutations. In D. melanogaster networks, we find a modest but significant enrichment of negative LD, consistent with the possibility of intranetwork negative synergistic epistasis.
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Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.,Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.,Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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30
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Zhang C, Zhang T, Luebert F, Xiang Y, Huang CH, Hu Y, Rees M, Frohlich MW, Qi J, Weigend M, Ma H. Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications. Mol Biol Evol 2021; 37:3188-3210. [PMID: 32652014 DOI: 10.1093/molbev/msaa160] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023] Open
Abstract
Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes and combined them with other data sets, representing all accepted orders and nearly all families of asterids. We show fully supported monophyly of asterids, Berberidopsidales as sister to asterids, monophyly of all orders except Icacinales, Aquifoliales, and Bruniales, and monophyly of all families except Icacinaceae and Ehretiaceae. Novel taxon placements benefited from the expanded sampling with living collections from botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous placements here are likely due to limited sampling and could be addressed in the future with relevant additional taxa. Using our well-resolved phylogeny as reference, divergence time estimates support an Aptian (Early Cretaceous) origin of asterids and the origin of all orders before the Cretaceous-Paleogene boundary. Ancestral state reconstruction at the family level suggests that the asterid ancestor was a woody terrestrial plant with simple leaves, bisexual, and actinomorphic flowers with free petals and free anthers, a superior ovary with a style, and drupaceous fruits. Whole-genome duplication (WGD) analyses provide strong evidence for 33 WGDs in asterids and one in Berberidopsidales, including four suprafamilial and seven familial/subfamilial WGDs. Our results advance the understanding of asterid phylogeny and provide numerous novel evolutionary insights into their diversification and morphological evolution.
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Affiliation(s)
- Caifei Zhang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Taikui Zhang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Federico Luebert
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany.,Department of Silviculture and Nature Conservation, University of Chile, Santiago, Chile
| | - Yezi Xiang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Mathew Rees
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | | | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Maximilian Weigend
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Hong Ma
- Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
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31
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Kerwin RE, Sweigart AL. Rampant Misexpression in a Mimulus (Monkeyflower) Introgression Line Caused by Hybrid Sterility, Not Regulatory Divergence. Mol Biol Evol 2021; 37:2084-2098. [PMID: 32196085 PMCID: PMC7306685 DOI: 10.1093/molbev/msaa071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Divergence in gene expression regulation is common between closely related species and may give rise to incompatibilities in their hybrid progeny. In this study, we investigated the relationship between regulatory evolution within species and reproductive isolation between species. We focused on a well-studied case of hybrid sterility between two closely related yellow monkeyflower species, Mimulus guttatus and Mimulus nasutus, that is caused by two epistatic loci, hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2). We compared genome-wide transcript abundance across male and female reproductive tissues (i.e., stamens and carpels) from four genotypes: M. guttatus, M. nasutus, and sterile and fertile progeny from an advanced M. nasutus–M. guttatus introgression line carrying the hms1–hms2 incompatibility. We observed substantial variation in transcript abundance between M. guttatus and M. nasutus, including distinct but overlapping patterns of tissue-biased expression, providing evidence for regulatory divergence between these species. We also found rampant genome-wide misexpression, but only in the affected tissues (i.e., stamens) of sterile introgression hybrids carrying incompatible alleles at hms1 and hms2. Examining patterns of allele-specific expression in sterile and fertile introgression hybrids, we found evidence for interspecific divergence in cis- and trans-regulation, including compensatory cis–trans mutations likely to be driven by stabilizing selection. Nevertheless, species divergence in gene regulatory networks cannot explain the vast majority of the gene misexpression we observe in Mimulus introgression hybrids, which instead likely manifests as a downstream consequence of sterility itself.
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Affiliation(s)
- Rachel E Kerwin
- Department of Genetics, University of Georgia, Athens, GA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
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32
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Zheng T, Li P, Li L, Zhang Q. Research advances in and prospects of ornamental plant genomics. HORTICULTURE RESEARCH 2021; 8:65. [PMID: 33790259 PMCID: PMC8012582 DOI: 10.1038/s41438-021-00499-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.
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Affiliation(s)
- Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus. Commun Biol 2021; 4:327. [PMID: 33712659 PMCID: PMC7954805 DOI: 10.1038/s42003-021-01795-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/05/2021] [Indexed: 01/24/2023] Open
Abstract
Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments. Vallejo-Marín et al. combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. They found that M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range, and hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide.
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Wang X, An Y, Xu P, Xiao J. Functioning of PPR Proteins in Organelle RNA Metabolism and Chloroplast Biogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:627501. [PMID: 33633768 PMCID: PMC7900629 DOI: 10.3389/fpls.2021.627501] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/04/2021] [Indexed: 05/05/2023]
Abstract
The pentatricopeptide repeat (PPR) proteins constitute one of the largest nuclear-encoded protein families in higher plants, with over 400 members in most sequenced plant species. The molecular functions of these proteins and their physiological roles during plant growth and development have been widely studied. Generally, there is mounting evidence that PPR proteins are involved in the post-transcriptional regulation of chloroplast and/or mitochondrial genes, including RNA maturation, editing, intron splicing, transcripts' stabilization, and translation initiation. The cooperative action of RNA metabolism has profound effects on the biogenesis and functioning of both chloroplasts and mitochondria and, consequently, on the photosynthesis, respiration, and development of plants and their environmental responses. In this review, we summarize the latest research on PPR proteins, specifically how they might function in the chloroplast, by documenting their mechanism of molecular function, their corresponding RNA targets, and their specific effects upon chloroplast biogenesis and host organisms.
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Affiliation(s)
- Xinwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yaqi An
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Pan Xu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jianwei Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Jianwei Xiao,
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Xu W, Zhang L, Cunningham AB, Li S, Zhuang H, Wang Y, Liu A. Blue genome: chromosome-scale genome reveals the evolutionary and molecular basis of indigo biosynthesis in Strobilanthes cusia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:864-879. [PMID: 32981147 DOI: 10.1111/tpj.14992] [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: 03/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Natural plant dyes have been developed and used across many traditional societies worldwide. The blue pigment indigo has seen widespread usage across South America, Egypt, Europe, India and China for thousands of years, mainly extracted from indigo-rich plants. The utilization and genetic engineering of indigo in industries and ethnobotanical studies on the effects of cultural selection on plant domestication are limited due to lack of relevant genetic and genomic information of dye plants. Strobilanthes cusia (Acanthaceae) is a typical indigo-rich plant important to diverse ethnic cultures in many regions of Asia. Here we present a chromosome-scale genome for S. cusia with a genome size of approximately 865 Mb. About 79% of the sequences were identified as repetitive sequences and 32 148 protein-coding genes were annotated. Metabolic analysis showed that the main indigoid pigments (indican, indigo and indirubin) were mainly synthesized in the leaves and stems of S. cusia. Transcriptomic analysis revealed that the expression level of genes encoding metabolic enzymes such as monooxygenase, uridine diphosphate-glycosyltransferase and β-glucosidase were significantly changed in leaves and stems compared with root tissues, implying their participation in indigo biosynthesis. We found that several gene families involved in indigo biosynthesis had undergone an expansion in number, with functional differentiation likely facilitating indigo biosynthesis in S. cusia. This study provides insight into the physiological and molecular bases of indigo biosynthesis, as well as providing genomic data that provide the basis for further study of S. cusia cultivation by Asia's traditional textile producers.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Libin Zhang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Anthony B Cunningham
- School of Veterinary and Life Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Shan Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Huifu Zhuang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Yuhua Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
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36
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Kelly LJ, Plumb WJ, Carey DW, Mason ME, Cooper ED, Crowther W, Whittemore AT, Rossiter SJ, Koch JL, Buggs RJA. Convergent molecular evolution among ash species resistant to the emerald ash borer. Nat Ecol Evol 2020; 4:1116-1128. [PMID: 32451426 PMCID: PMC7610378 DOI: 10.1038/s41559-020-1209-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 11/08/2022]
Abstract
Recent studies show that molecular convergence plays an unexpectedly common role in the evolution of convergent phenotypes. We exploited this phenomenon to find candidate loci underlying resistance to the emerald ash borer (EAB, Agrilus planipennis), the United States' most costly invasive forest insect to date, within the pan-genome of ash trees (the genus Fraxinus). We show that EAB-resistant taxa occur within three independent phylogenetic lineages. In genomes from these resistant lineages, we detect 53 genes with evidence of convergent amino acid evolution. Gene-tree reconstruction indicates that, for 48 of these candidates, the convergent amino acids are more likely to have arisen via independent evolution than by another process such as hybridization or incomplete lineage sorting. Seven of the candidate genes have putative roles connected to the phenylpropanoid biosynthesis pathway and 17 relate to herbivore recognition, defence signalling or programmed cell death. Evidence for loss-of-function mutations among these candidates is more frequent in susceptible species than in resistant ones. Our results on evolutionary relationships, variability in resistance, and candidate genes for defence response within the ash genus could inform breeding for EAB resistance, facilitating ecological restoration in areas invaded by this beetle.
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Affiliation(s)
- Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
| | - William J Plumb
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Royal Botanic Gardens, Kew, Richmond, UK
- Forestry Development Department, Teagasc, Dublin, Republic of Ireland
| | - David W Carey
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Mary E Mason
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Endymion D Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - William Crowther
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Alan T Whittemore
- United States Department of Agriculture, Agricultural Research Service, US National Arboretum, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jennifer L Koch
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
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37
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He Z, Xu S, Zhang Z, Guo W, Lyu H, Zhong C, Boufford DE, Duke NC, Shi S. Convergent adaptation of the genomes of woody plants at the land-sea interface. Natl Sci Rev 2020; 7:978-993. [PMID: 34692119 PMCID: PMC8289059 DOI: 10.1093/nsr/nwaa027] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/30/2020] [Accepted: 02/09/2020] [Indexed: 01/19/2023] Open
Abstract
Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.
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Affiliation(s)
- Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhang Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Haomin Lyu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve Administration, Haikou 571129, China
| | | | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD 4811, Australia
| | | | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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38
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Kooyers NJ, Donofrio A, Blackman BK, Holeski LM. The Genetic Architecture of Plant Defense Trade-offs in a Common Monkeyflower. J Hered 2020; 111:333-345. [DOI: 10.1093/jhered/esaa015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a quantitative trait loci (QTL) mapping experiment involving a cross between 2 populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy underlies correlations between defense and growth rate. However, there is a strong genetic correlation between levels of total PPGs and flowering time that is largely attributable to a single shared QTL. While this result suggests a role for pleiotropy/close linkage, several other QTLs also contribute to variation in total PPGs. Additionally, divergent PPG arsenals are influenced by a number of smaller-effect QTLs that each underlie variation in 1 or 2 PPGs. This result indicates that chemical defense arsenals can be finely adapted to biotic environments despite sharing a common biochemical precursor. Together, our results show correlations between defense and life-history traits are influenced by pleiotropy or genetic linkage, but genetic constraints may have limited impact on future evolutionary responses, as a substantial proportion of variation in each trait is controlled by independent loci.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA
- Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Abigail Donofrio
- Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA
| | - Liza M Holeski
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
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39
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Schwarzkopf EJ, Motamayor JC, Cornejo OE. Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations. BMC Genomics 2020; 21:332. [PMID: 32349675 PMCID: PMC7191684 DOI: 10.1186/s12864-020-6746-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated. Results Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo. Conclusions We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.
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Affiliation(s)
| | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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40
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Samuk K, Manzano-Winkler B, Ritz KR, Noor MAF. Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura. Curr Biol 2020; 30:1517-1528.e6. [PMID: 32275873 DOI: 10.1016/j.cub.2020.03.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/16/2019] [Accepted: 03/20/2020] [Indexed: 12/30/2022]
Abstract
While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8,000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short- and long-read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400 kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400 kb scale, recombination rate appears to vary largely genome-wide, rather than in specific intervals, and (3) interpopulation differences in recombination rate may be the result of local adaptation.
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Affiliation(s)
- Kieran Samuk
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | | | - Kathryn R Ritz
- Department of Biology, Duke University, Durham, NC 27708, USA
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41
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Guo H, Lackus ND, Köllner TG, Li R, Bing J, Wang Y, Baldwin IT, Xu S. Evolution of a Novel and Adaptive Floral Scent in Wild Tobacco. Mol Biol Evol 2020; 37:1090-1099. [PMID: 31808808 DOI: 10.1093/molbev/msz292] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many plants emit diverse floral scents that mediate plant-environment interactions and attain reproductive success. However, how plants evolve novel and adaptive biosynthetic pathways for floral volatiles remains unclear. Here, we show that in the wild tobacco, Nicotiana attenuata, a dominant species-specific floral volatile (benzyl acetone, BA) that attracts pollinators and deters florivore is synthesized by phenylalanine ammonia-lyase 4 (NaPAL4), isoflavone reductase 3 (NaIFR3), and chalcone synthase 3 (NaCHAL3). Transient expression of NaFIR3 alone in N. attenuata leaves is sufficient and necessary for ectopic foliar BA emissions, and coexpressing NaIFR3 with NaPAL4 and NaCHAL3 increased the BA emission levels. Independent changes in transcription of NaPAL4 and NaCHAL3 contributed to intraspecific variations of floral BA emission. However, among species, the gain of expression of NaIFR3 resulted in the biosynthesis of BA, which was only found in N. attenuata. This study suggests that novel metabolic pathways associated with adaptation can arise via reconfigurations of gene expression.
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Affiliation(s)
- Han Guo
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nathalie D Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ran Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Julia Bing
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yangzi Wang
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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42
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Ding B, Patterson EL, Holalu SV, Li J, Johnson GA, Stanley LE, Greenlee AB, Peng F, Bradshaw HD, Blinov ML, Blackman BK, Yuan YW. Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns. Curr Biol 2020; 30:802-814.e8. [PMID: 32155414 PMCID: PMC7156294 DOI: 10.1016/j.cub.2019.12.067] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 11/19/2022]
Abstract
Many organisms exhibit visually striking spotted or striped pigmentation patterns. Developmental models predict that such spatial patterns can form when a local autocatalytic feedback loop and a long-range inhibitory feedback loop interact. At its simplest, this self-organizing network only requires one self-activating activator that also activates a repressor, which inhibits the activator and diffuses to neighboring cells. However, the molecular activators and inhibitors fully fitting this versatile model remain elusive in pigmentation systems. Here, we characterize an R2R3-MYB activator and an R3-MYB repressor in monkeyflowers (Mimulus). Through experimental perturbation and mathematical modeling, we demonstrate that the properties of these two proteins correspond to an activator-inhibitor pair in a two-component, reaction-diffusion system, explaining the formation of dispersed anthocyanin spots in monkeyflower petals. Notably, disrupting this pattern impacts pollinator visitation. Thus, subtle changes in simple activator-inhibitor systems are likely essential contributors to the evolution of the remarkable diversity of pigmentation patterns in flowers.
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Affiliation(s)
- Baoqing Ding
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Erin L Patterson
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA; Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Srinidhi V Holalu
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA; Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Jingjian Li
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA; College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Grace A Johnson
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA
| | - Lauren E Stanley
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Anna B Greenlee
- Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Foen Peng
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
| | - H D Bradshaw
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
| | - Michael L Blinov
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA; Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA.
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, 67 North Eagleville Road, Storrs, CT 06269, USA.
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Tang CY, Li S, Wang YT, Wang X. Comparative genome/transcriptome analysis probes Boraginales' phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin/shikonin core pathway. Mol Ecol Resour 2019; 20:228-241. [PMID: 31625679 DOI: 10.1111/1755-0998.13104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 12/27/2022]
Abstract
Boraginales (the forget-me-not order) is a core group within the lamiids clade. However, until now, no genome from Boraginales has been reported, and published transcriptomes are also rare. Here, we report the first Boraginales species de novo genome (i.e. Echium plantagineum genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales/Gentianales clade than the Lamiales clade, at least based on the single-copy orthologous genes from genome/transcriptome data; (ii) after the gamma (γ) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and O-acyl transferase.
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Affiliation(s)
- Cheng-Yi Tang
- School of the Environment, Nanjing University, Nanjing, China
| | - Song Li
- School of the Environment, Nanjing University, Nanjing, China.,Biomarker Technologies Corporation, Beijing, China
| | | | - Xi Wang
- Biomarker Technologies Corporation, Beijing, China
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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45
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Ho EKH, Bartkowska M, Wright SI, Agrawal AF. Population genomics of the facultatively asexual duckweed Spirodela polyrhiza. THE NEW PHYTOLOGIST 2019; 224:1361-1371. [PMID: 31298732 DOI: 10.1111/nph.16056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection ineffective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level. The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.
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Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Magdalena Bartkowska
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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Li Z, Vickrey TL, McNally MG, Sato SJ, Clemente TE, Mower JP. Assessing Anthocyanin Biosynthesis in Solanaceae as a Model Pathway for Secondary Metabolism. Genes (Basel) 2019; 10:genes10080559. [PMID: 31349565 PMCID: PMC6723469 DOI: 10.3390/genes10080559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 01/25/2023] Open
Abstract
Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI annotation pipeline generated more and longer FBP annotations on average than genome-specific annotation pipelines. The pattern of diversification of each enzyme among asterids was assessed by phylogenetic analysis, showing that the CHS superfamily encompasses a large paralogous family of ancient and recent duplicates, whereas other FBP enzymes have diversified via recent duplications in particular lineages. Heterologous expression of a pansy F3′5′H gene in tobacco changed flower color from pink to dark purple, demonstrating that anthocyanin production can be predictably modified using reverse genetics. These results suggest that the Solanaceae FBP could be an ideal system to model genotype-to-phenotype interactions for secondary metabolism.
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Affiliation(s)
- Zuo Li
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Trisha L Vickrey
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Moira G McNally
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Biology Department, University of Jamestown, Jamestown, ND 58405, USA
| | - Shirley J Sato
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - Tom Elmo Clemente
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA.
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA.
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Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. Chromosoma 2019; 128:279-296. [PMID: 31332531 DOI: 10.1007/s00412-019-00718-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023]
Abstract
During meiosis, DNA double-strand breaks are initiated by the topoisomerase-like enzyme SPO11 and are repaired by inter-sister chromatid and inter-homologue DNA repair pathways. Genome-wide maps of initiating DNA double-strand breaks and inter-homologue repair events are now available for a number of mammalian, fungal and plant species. In mammals, PRDM9 specifies the location of meiotic recombination initiation via recognition of specific DNA sequence motifs by its C2H2 zinc finger array. In fungi and plants, meiotic recombination appears to be initiated less discriminately in accessible chromatin, including at gene promoters. Generally, meiotic crossover is suppressed in highly repetitive genomic regions that are made up of transposable elements (TEs), to prevent deleterious non-allelic homologous recombination events. However, recent and older studies have revealed intriguing relationships between meiotic recombination initiation and repair, and transposable elements. For instance, gene conversion events have been detected in maize centromeric retroelements, mouse MULE-MuDR DNA transposons undergo substantial meiotic recombination initiation, Arabidopsis Helitron TEs are among the hottest of recombination initiation hotspots, and human TE sequences can modify the crossover rate at adjacent PRDM9 motifs in cis. Here, we summarize the relationship between meiotic recombination and TEs, discuss recent insights from highly divergent eukaryotes and highlight outstanding questions in the field.
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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Misra VA, Wafula EK, Wang Y, dePamphilis CW, Timko MP. Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism. BMC PLANT BIOLOGY 2019; 19:196. [PMID: 31088371 PMCID: PMC6515653 DOI: 10.1186/s12870-019-1786-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 04/17/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Root parasitic weeds are a major constraint to crop production worldwide causing significant yearly losses in yield and economic value. These parasites cause their destruction by attaching to their hosts with a unique organ, the haustorium, that allows them to obtain the nutrients (sugars, amino acids, etc.) needed to complete their lifecycle. Parasitic weeds differ in their nutritional requirements and degree of host dependency and the differential expression of sugar transporters is likely to be a critical component in the parasite's post-attachment survival. RESULTS We identified gene families encoding monosaccharide transporters (MSTs), sucrose transporters (SUTs), and SWEETs (Sugars Will Eventually be Exported Transporters) in three root-parasitic weeds differing in host dependency: Triphysaria versicolor (facultative hemiparasite), Phelipanche aegyptiaca (holoparasite), and Striga hermonthica (obligate hemiparasite). The phylogenetic relationship and differential expression profiles of these genes throughout parasite development were examined to uncover differences existing among parasites with different levels of host dependence. Differences in estimated gene numbers are found among the three parasites, and orthologs within the different sugar transporter gene families are found to be either conserved among the parasites in their expression profiles throughout development, or to display parasite-specific differences in developmentally-timed expression. For example, MST genes in the pGLT clade express most highly before host connection in Striga and Triphysaria but not Phelipanche, whereas genes in the MST ERD6-like clade are highly expressed in the post-connection growth stages of Phelipanche but highest in the germination and reproduction stages in Striga. Whether such differences reflect changes resulting from differential host dependence levels is not known. CONCLUSIONS While it is tempting to speculate that differences in estimated gene numbers and expression profiles among members of MST, SUT and SWEET gene families in Phelipanche, Striga and Triphysaria reflect the parasites' levels of host dependence, additional evidence that altered transporter gene expression is causative versus consequential is needed. Our findings identify potential targets for directed manipulation that will allow for a better understanding of the nutrient transport process and perhaps a means for controlling the devastating effects of these parasites on crop productivity.
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Affiliation(s)
- Vikram A. Misra
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
| | - Eric K. Wafula
- Department of Biology, Penn State University, University Park, PA 16802 USA
| | - Yu Wang
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
- Present Address: Center for Quantitative Sciences, Vanderbilt University, 2220 Pierce Avenue, 571 Preston Research Building, Nashville, TN 37232-6848 USA
| | | | - Michael P. Timko
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
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Choudhury RR, Rogivue A, Gugerli F, Parisod C. Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes. Mol Ecol 2019; 28:1550-1562. [DOI: 10.1111/mec.15014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/26/2018] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aude Rogivue
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
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