1
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Zhang DQ, Liu XY, Qiu LF, Liu ZR, Yang YP, Huang L, Wang SY, Zhang JQ. Two chromosome-level genome assemblies of Rhodiola shed new light on genome evolution in rapid radiation and evolution of the biosynthetic pathway of salidroside. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:464-482. [PMID: 37872890 DOI: 10.1111/tpj.16501] [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: 06/20/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
Rhodiola L. is a genus that has undergone rapid radiation in the mid-Miocene and may represent a typic case of adaptive radiation. Many species of Rhodiola have also been widely used as an important adaptogen in traditional medicines for centuries. However, a lack of high-quality chromosome-level genomes hinders in-depth study of its evolution and biosynthetic pathway of secondary metabolites. Here, we assembled two chromosome-level genomes for two Rhodiola species with different chromosome number and sexual system. The assembled genome size of R. chrysanthemifolia (2n = 14; hermaphrodite) and R. kirilowii (2n = 22; dioecious) were of 402.67 and 653.62 Mb, respectively, with approximately 57.60% and 69.22% of transposable elements (TEs). The size difference between the two genomes was mostly due to proliferation of long terminal repeat-retrotransposons (LTR-RTs) in the R. kirilowii genome. Comparative genomic analysis revealed possible gene families responsible for high-altitude adaptation of Rhodiola, including a homolog of plant cysteine oxidase 2 gene of Arabidopsis thaliana (AtPCO2), which is part of the core molecular reaction to hypoxia and contributes to the stability of Group VII ethylene response factors (ERF-VII). We found extensive chromosome fusion/fission events and structural variations between the two genomes, which might have facilitated the initial rapid radiation of Rhodiola. We also identified candidate genes in the biosynthetic pathway of salidroside. Overall, our results provide important insights into genome evolution in plant rapid radiations, and possible roles of chromosome fusion/fission and structure variation played in rapid speciation.
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Affiliation(s)
- Dan-Qing Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Xiao-Ying Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Lin-Feng Qiu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Zhao-Rui Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Ya-Peng Yang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Long Huang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Shi-Yu Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Jian-Qiang Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
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2
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Wang B, Liang N, Shen X, Xie Z, Zhang L, Tian B, Yuan Y, Guo J, Zhang X, Wei F, Wei X. Cytological and transcriptomic analyses provide insights into the pollen fertility of synthetic allodiploid Brassica juncea hybrids. PLANT CELL REPORTS 2023; 43:23. [PMID: 38150101 DOI: 10.1007/s00299-023-03089-4] [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: 07/16/2023] [Accepted: 10/10/2023] [Indexed: 12/28/2023]
Abstract
KEY MESSAGE Imbalanced chromosomes and cell cycle arrest, along with down-regulated genes in DNA damage repair and sperm cell differentiation, caused pollen abortion in synthetic allodiploid Brassica juncea hybrids. Interspecific hybridization is considered to be a major pathway for species formation and evolution in angiosperms, but the occurrence of pollen abortion in the hybrids is common, prompting us to recheck male gamete development in allodiploid hybrids after the initial combination of different genomes. Here, we investigated the several key meiotic and mitotic events during pollen development using the newly synthesised allodiploid B. juncea hybrids (AB, 2n = 2× = 18) as a model system. Our results demonstrated the partial synapsis and pairing of non-homologous chromosomes concurrent with chaotic spindle assembly, affected chromosome assortment and distribution during meiosis, which finally caused difference in genetic constitution amongst the final tetrads. The mitotic cell cycle arrest during microspore development resulted in the production of anucleate pollen cells. Transcription analysis showed that sets of key genes regulating cyclin (CYCA1;2 and CYCA2;3), DNA damage repair (DMC1, NBS1 and MMD1), and ubiquitin-proteasome pathway (SINAT4 and UBC) were largely downregulated at the early pollen meiosis stages, and those genes involved in sperm cell differentiation (DUO1, PIRL1, PIRL9 and LBD27) and pollen wall synthesis (PME48, VGDH11 and COBL10) were mostly repressed at the late pollen mitosis stages in the synthetic allodiploid B. juncea hybrids (AB). In conclusion, this study elucidated the related mechanisms affecting pollen fertility during male gametophyte development at the cytological and transcriptomic levels in the synthetic allodiploid B. juncea hybrids.
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Affiliation(s)
- Boyang Wang
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Niannian Liang
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Xiaohan Shen
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Luyue Zhang
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Jialin Guo
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.
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3
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Venney CJ, Anastasiadi D, Wellenreuther M, Bernatchez L. The Evolutionary Complexities of DNA Methylation in Animals: From Plasticity to Genetic Evolution. Genome Biol Evol 2023; 15:evad216. [PMID: 38015807 PMCID: PMC10701099 DOI: 10.1093/gbe/evad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/22/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of DNA methylation in plastic responses to environmental change and evolutionary dynamics is increasingly recognized. Here, we provide a Perspective piece on the diverse roles of DNA methylation on broad evolutionary timescales, including (i) short-term transient acclimation, (ii) stable phenotypic evolution, and (iii) genomic evolution. We show that epigenetic responses vary along a continuum, ranging from short-term acclimatory responses in variable environments within a generation to long-term modifications in populations and species. DNA methylation thus unlocks additional potential for organisms to rapidly acclimate to their environment over short timeframes. If these changes affect fitness, they can circumvent the need for adaptive changes at the genome level. However, methylation has a complex reciprocal relationship with genetic variation as it can be genetically controlled, yet it can also induce point mutations and contribute to genomic evolution. When habitats remain constant over many generations, or populations are separated across habitats, initially plastic phenotypes can become hardwired through epigenetically facilitated mutagenesis. It remains unclear under what circumstances plasticity contributes to evolutionary outcomes, and when plastic changes will become permanently encoded into genotype. We highlight how studies investigating the evolution of epigenetic plasticity need to carefully consider how plasticity in methylation state could evolve among different evolutionary scenarios, the possible phenotypic outcomes, its effects on genomic evolution, and the proximate energetic and ultimate fitness costs of methylation. We argue that accumulating evidence suggests that DNA methylation can contribute toward evolution on various timescales, spanning a continuum from acclimatory plasticity to genomic evolution.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
| | - Dafni Anastasiadi
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
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4
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [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: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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5
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Reifová R, Ament-Velásquez SL, Bourgeois Y, Coughlan J, Kulmuni J, Lipinska AP, Okude G, Stevison L, Yoshida K, Kitano J. Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives. Cold Spring Harb Perspect Biol 2023; 15:a041607. [PMID: 37696577 PMCID: PMC10547394 DOI: 10.1101/cshperspect.a041607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | | | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34090 Montpellier, France
| | - Jenn Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Jonna Kulmuni
- Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, 1012 Amsterdam, The Netherlands
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, 00100 Helsinki, Finland
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076 Tuebingen, Germany
- CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Genta Okude
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Laurie Stevison
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Kohta Yoshida
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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6
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Ding X, Zhang Y, Li D, Xu J, Wu C, Cui X, Sun Y. Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus. BMC Genom Data 2023; 24:45. [PMID: 37573319 PMCID: PMC10422732 DOI: 10.1186/s12863-023-01141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream, BSB, 2n = 48) and Culter alburnus (Topmouth culter, TC, 2n = 48) was achieved to establish hybrid lineages (BT and TB), which provide valuable materials for exploring the mechanisms of distant hybridization fertility. In this study, the gonadal tissue transcriptomes of BSB, TC, BT-F1, and TB-F1 were sequenced using Illumina high-throughput sequencing technology to analyze the reproductive characteristics of BT and TB. RESULTS Differential gene expression analysis showed that the differentially expressed genes in BT vs BSB and BT vs TC were mainly enriched in signaling pathways not directly associated with meiosis. While, the differentially expressed genes of TB vs BSB and TB vs TC were mainly enriched in pathways related to meiosis, and most of them were down-regulated, indicating that meiosis is suppressed in TB. Under-dominance (UD) genes were enriched in pathways related to meiosis and DNA repair in TB. Over-dominance (OD) genes were enriched in MAPK signaling pathway, expression level dominance-BSB (ELD-B) genes were enriched in pathways related to steroid hormone synthesis and expression level dominance-TC (ELD-T) genes were not significantly enriched in any pathway in both BT and TB. CONCLUSIONS These results suggest that meiotic progression may not be affected in BT, whereas it is clearly inhibited in TB. Offspring of M. amblycephala maternal parent may have better genomic compatibility and fertility. Our study provides important information on the molecular mechanisms of breaking reproductive isolation in distantly hybridized fertile lineages.
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Affiliation(s)
- Xue Ding
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Yifei Zhang
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Die Li
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Jia Xu
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fishes, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xiaojuan Cui
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
| | - Yuandong Sun
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
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7
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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8
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Shi Z, Liu G, Jiang H, Shi S, Zhang X, Deng Y, Chen Y. Activation of P53 pathway contributes to Xenopus hybrid inviability. Proc Natl Acad Sci U S A 2023; 120:e2303698120. [PMID: 37186864 PMCID: PMC10214167 DOI: 10.1073/pnas.2303698120] [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: 03/08/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Hybrid incompatibility as a kind of reproductive isolation contributes to speciation. The nucleocytoplasmic incompatibility between Xenopus tropicalis eggs and Xenopus laevis sperm (te×ls) leads to specific loss of paternal chromosomes 3L and 4L. The hybrids die before gastrulation, of which the lethal causes remain largely unclear. Here, we show that the activation of the tumor suppressor protein P53 at late blastula stage contributes to this early lethality. We find that in stage 9 embryos, P53-binding motif is the most enriched one in the up-regulated Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) peaks between te×ls and wild-type X. tropicalis controls, which correlates with an abrupt stabilization of P53 protein in te×ls hybrids at stage 9. Inhibition of P53 activity via either tp53 knockout or overexpression of a dominant-negative P53 mutant or Murine double minute 2 proto-oncogene (Mdm2), a negative regulator of P53, by mRNA injection can rescue the te×ls early lethality. Our results suggest a causal function of P53 on hybrid lethality prior to gastrulation.
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Affiliation(s)
- Zhaoying Shi
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Guanghui Liu
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Hao Jiang
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Songyuan Shi
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Xuan Zhang
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Yi Deng
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Yonglong Chen
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
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9
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Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A. Satellite DNA evolution in Corvoidea inferred from short and long reads. Mol Ecol 2023; 32:1288-1305. [PMID: 35488497 DOI: 10.1111/mec.16484] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK
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10
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Yoshida K, Rödelsperger C, Röseler W, Riebesell M, Sun S, Kikuchi T, Sommer RJ. Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nat Ecol Evol 2023; 7:424-439. [PMID: 36717742 PMCID: PMC9998273 DOI: 10.1038/s41559-022-01980-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 12/29/2022] [Indexed: 02/01/2023]
Abstract
Large-scale genome-structural evolution is common in various organisms. Recent developments in speciation genomics revealed the importance of inversions, whereas the role of other genome-structural rearrangements, including chromosome fusions, have not been well characterized. We study genomic divergence and reproductive isolation of closely related nematodes: the androdioecious (hermaphroditic) model Pristionchus pacificus and its dioecious sister species Pristionchus exspectatus. A chromosome-level genome assembly of P. exspectatus using single-molecule and Hi-C sequencing revealed a chromosome-wide rearrangement relative to P. pacificus. Strikingly, genomic characterization and cytogenetic studies including outgroup species Pristionchus occultus indicated two independent fusions involving the same chromosome, ChrIR, between these related species. Genetic linkage analysis indicated that these fusions altered the chromosome-wide pattern of recombination, resulting in large low-recombination regions that probably facilitated the coevolution between some of the ~14.8% of genes across the entire genomes. Quantitative trait locus analyses for hybrid sterility in all three sexes revealed that major quantitative trait loci mapped to the fused chromosome ChrIR. While abnormal chromosome segregations of the fused chromosome partially explain hybrid female sterility, hybrid-specific recombination that breaks linkage of genes in the low-recombination region was associated with hybrid male sterility. Thus, recent chromosome fusions repatterned recombination rate and drove reproductive isolation during Pristionchus speciation.
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Affiliation(s)
- Kohta Yoshida
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Waltraud Röseler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Metta Riebesell
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
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11
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Shin H, Park JE, Park HR, Choi WL, Yu SH, Koh W, Kim S, Soh HY, Waminal NE, Belandres HR, Lim JY, Yi G, Ahn JH, Kim J, Kim Y, Koo N, Kim K, Perumal S, Kang T, Kim J, Jang H, Kang DH, Kim YS, Jeong H, Yang J, Song S, Park S, Kim JA, Lim YP, Park B, Hsieh T, Yang T, Choi D, Kim HH, Lee S, Huh JH. Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae. THE NEW PHYTOLOGIST 2022; 235:743-758. [PMID: 35403705 PMCID: PMC9320894 DOI: 10.1111/nph.18155] [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: 11/25/2021] [Accepted: 03/28/2022] [Indexed: 05/15/2023]
Abstract
Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Jeong Eun Park
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hye Rang Park
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Woo Lee Choi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Seung Hwa Yu
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Wonjun Koh
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Seungill Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Department of Environmental HorticultureUniversity of SeoulSeoul02504South Korea
| | - Hye Yeon Soh
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Nomar Espinosa Waminal
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Hadassah Roa Belandres
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Joo Young Lim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Gibum Yi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Jong Hwa Ahn
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - June‐Sik Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Yong‐Min Kim
- Korea Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141South Korea
| | - Namjin Koo
- Korea Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141South Korea
| | - Kyunghee Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Sampath Perumal
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Taegu Kang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Junghyo Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Hosung Jang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Dong Hyun Kang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Ye Seul Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hyeon‐Min Jeong
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Junwoo Yang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Somin Song
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Suhyoung Park
- Department of Horticultural Crop ResearchNational Institute of Horticultural and Herbal ScienceRural Development AdministrationWanjuJeollabuk‐do55365South Korea
| | - Jin A. Kim
- Department of Agricultural BiotechnologyNational Academy of Agricultural ScienceRural Development AdministrationJeonjuJeollabuk‐do54874South Korea
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeon34134South Korea
| | | | - Tzung‐Fu Hsieh
- Plants for Human Health InstituteNorth Carolina State UniversityNorth Carolina Research CampusKannapolisNC27695USA
| | - Tae‐Jin Yang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Doil Choi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hyun Hee Kim
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Soo‐Seong Lee
- BioBreeding InstituteAnseongGyeonggi‐do17544South Korea
| | - Jin Hoe Huh
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
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12
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Hodel RGJ, Massatti R, Knowles LL. Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges. Mol Ecol 2022; 31:3722-3737. [PMID: 35560840 PMCID: PMC9327521 DOI: 10.1111/mec.16502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.
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Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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13
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Kwon T, Kim K, Caetano-Anolles K, Sung S, Cho S, Jeong C, Hanotte O, Kim H. Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle. BMC Biol 2022; 20:20. [PMID: 35039029 PMCID: PMC8764764 DOI: 10.1186/s12915-021-01206-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Africa is an important watershed in the genetic history of domestic cattle, as two lineages of modern cattle, Bos taurus and B. indicus, form distinct admixed cattle populations. Despite the predominant B. indicus nuclear ancestry of African admixed cattle, B. indicus mitochondria have not been found on the continent. This discrepancy between the mitochondrial and nuclear genomes has been previously hypothesized to be driven by male-biased introgression of Asian B. indicus into ancestral African B. taurus. Given that this hypothesis mandates extreme demographic assumptions relying on random genetic drift, we propose a novel hypothesis of selection induced by mitonuclear incompatibility and assess these hypotheses with regard to the current genomic status of African admixed cattle. Results By analyzing 494 mitochondrial and 235 nuclear genome sequences, we first confirmed the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle: the absence of B. indicus mitochondria and the predominant B. indicus autosomal ancestry. We applied approximate Bayesian computation (ABC) to assess the posterior probabilities of two selection hypotheses given this observation. The results of ABC indicated that the model assuming both male-biased B. indicus introgression and selection induced by mitonuclear incompatibility explains the current genomic discrepancy most accurately. Subsequently, we identified selection signatures at autosomal loci interacting with mitochondria that are responsible for integrity of the cellular respiration system. By contrast with B. indicus-enriched genome ancestry of African admixed cattle, local ancestries at these selection signatures were enriched with B. taurus alleles, concurring with the key expectation of selection induced by mitonuclear incompatibility. Conclusions Our findings support the current genome status of African admixed cattle as a potential outcome of male-biased B. indicus introgression, where mitonuclear incompatibility exerted selection pressure against B. indicus mitochondria. This study provides a novel perspective on African cattle demography and supports the role of mitonuclear incompatibility in the hybridization of mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01206-x.
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Affiliation(s)
- Taehyung Kwon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,eGnome, Inc, Seoul, South Korea
| | | | | | | | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, UK. .,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia. .,The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, UK.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea. .,eGnome, Inc, Seoul, South Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.
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14
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15
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Palmer MCL, Neudorf NM, Farrell AC, Razi T, Lichtensztejn Z, McManus KJ. The F-box protein, FBXO7 is required to maintain chromosome stability in humans. Hum Mol Genet 2021; 31:1471-1486. [PMID: 34791250 PMCID: PMC9071473 DOI: 10.1093/hmg/ddab330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 11/19/2022] Open
Abstract
Despite the high morbidity and mortality rates associated with colorectal cancer (CRC), the aberrant genes and mechanisms driving CRC pathogenesis remain poorly understood. Chromosome instability (CIN), or ongoing changes in chromosome numbers, is a predominant form of genome instability associated with ~85% of CRCs, suggesting it may be a key mechanism driving CRC oncogenesis. CIN enables the acquisition of copy number alterations conferring selective growth, proliferation and survival advantages that promote cellular transformation. Despite these associations, the aberrant genes underlying CIN remain largely unknown. Candidate CIN gene FBXO7 encodes an F-box protein, a subunit of the SKP1-CUL1-FBOX (SCF) complex that confers substrate specificity to the complex and targets proteins for subsequent degradation by the 26S proteasome. Recently, the genes encoding the three core SCF complex members were identified as CIN genes; however, it is unknown whether F-box proteins exhibit similar integral roles in maintaining chromosome stability. Using short- small interfering RNA (siRNA) and long- (CRISPR/Cas9) term approaches, we show that reduced FBXO7 expression induces CIN in various colonic epithelial cell contexts, whereas FBXO7 knockout clones also exhibit hallmarks associated with cellular transformation, namely increased clonogenic and anchorage-independent growth. Collectively, these data demonstrate that FBXO7 is required to maintain genome stability identifying FBXO7 a novel CIN gene whose reduced expression may contribute to CRC development and progression.
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Affiliation(s)
- Michaela C L Palmer
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Nicole M Neudorf
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ally C Farrell
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Tooba Razi
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Zelda Lichtensztejn
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kirk J McManus
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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16
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Bendixsen DP, Peris D, Stelkens R. Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:742894. [PMID: 37744091 PMCID: PMC10512264 DOI: 10.3389/ffunb.2021.742894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
Abstract
The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.
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Affiliation(s)
- Devin P. Bendixsen
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Health, Valencian International University, Valencia, Spain
| | - Rike Stelkens
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
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17
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Serrato-Capuchina A, D’Agostino ERR, Peede D, Roy B, Isbell K, Wang J, Matute DR. P-elements strengthen reproductive isolation within the Drosophila simulans species complex. Evolution 2021; 75:2425-2440. [PMID: 34463356 PMCID: PMC8772388 DOI: 10.1111/evo.14319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. We also find that another TE, I-element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emmanuel R. R. D’Agostino
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Kristin Isbell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Daniel R. Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
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18
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Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
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19
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Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
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20
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Marsit S, Hénault M, Charron G, Fijarczyk A, Landry CR. The neutral rate of whole-genome duplication varies among yeast species and their hybrids. Nat Commun 2021; 12:3126. [PMID: 34035259 PMCID: PMC8149824 DOI: 10.1038/s41467-021-23231-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/19/2021] [Indexed: 11/09/2022] Open
Abstract
Hybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD may allow hybrids to thrive by increasing fitness, restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. Here we show, by measuring the spontaneous rate of WGD of more than 1300 yeast crosses evolved under relaxed selection, that some genotypes or combinations of genotypes are more prone to WGD, including some hybrids between closely related species. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.
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Affiliation(s)
- S Marsit
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada.
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada.
| | - M Hénault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada
| | - G Charron
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - A Fijarczyk
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada
| | - C R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada.
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada.
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21
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Badaeva ED, Chikida NN, Fisenko AN, Surzhikov SA, Belousova MK, Özkan H, Dragovich AY, Kochieva EZ. Chromosome and Molecular Analyses Reveal Significant Karyotype Diversity and Provide New Evidence on the Origin of Aegilops columnaris. PLANTS (BASEL, SWITZERLAND) 2021; 10:956. [PMID: 34064905 PMCID: PMC8151338 DOI: 10.3390/plants10050956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/28/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022]
Abstract
Aegilops columnaris Zhuk. is tetraploid grass species (2n = 4x = 28, UcUcXcXc) closely related to Ae. neglecta and growing in Western Asia and a western part of the Fertile Crescent. Genetic diversity of Ae. columnaris was assessed using C-banding, FISH, nuclear and chloroplast (cp) DNA analyses, and gliadin electrophoresis. Cytogenetically Ae. columnaris was subdivided into two groups, C-I and C-II, showing different karyotype structure, C-banding, and FISH patterns. C-I group was more similar to Ae. neglecta. All types of markers revealed significant heterogeneity in C-II group, although group C-I was also polymorphic. Two chromosomal groups were consistent with plastogroups identified in a current study based on sequencing of three chloroplast intergenic spacer regions. The similarity of group C-I of Ae. columnaris with Ae. neglecta and their distinctness from C-II indicate that divergence of the C-I group was associated with minor genome modifications. Group C-II could emerge from C-I relatively recently, probably due to introgression from another Aegilops species followed by a reorganization of the parental genomes. Most C-II accessions were collected from a very narrow geographic region, and they might originate from a common ancestor. We suggest that the C-II group is at the initial stage of species divergence and undergoing an extensive speciation process.
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Affiliation(s)
- Ekaterina D. Badaeva
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, GSP–1, 119991 Moscow, Russia; (A.N.F.); (A.Y.D.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Street 34, GSP–1, 119991 Moscow, Russia;
| | - Nadezhda N. Chikida
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Bolshaya Morskaya Street 44, 190121 St. Petersburg, Russia; (N.N.C.); (M.K.B.)
| | - Andrey N. Fisenko
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, GSP–1, 119991 Moscow, Russia; (A.N.F.); (A.Y.D.)
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Street 34, GSP–1, 119991 Moscow, Russia;
| | - Maria K. Belousova
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Bolshaya Morskaya Street 44, 190121 St. Petersburg, Russia; (N.N.C.); (M.K.B.)
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, 01330 Adana, Turkey;
| | - Alexandra Y. Dragovich
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, GSP–1, 119991 Moscow, Russia; (A.N.F.); (A.Y.D.)
| | - Elena Z. Kochieva
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 60 let Oktjabrya Prospect 7, Build. 1, 117312 Moscow, Russia;
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22
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Bautista C, Marsit S, Landry CR. Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions. Evol Appl 2021; 14:758-769. [PMID: 33767750 PMCID: PMC7980265 DOI: 10.1111/eva.13155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022] Open
Abstract
Hybridization may increase the probability of adaptation to extreme stresses. This advantage could be caused by an increased genome plasticity in hybrids, which could accelerate the search for adaptive mutations. High ultraviolet (UV) radiation is a particular challenge in terms of adaptation because it affects the viability of organisms by directly damaging DNA, while also challenging future generations by increasing mutation rate. Here we test whether hybridization accelerates adaptive evolution in response to DNA damage, using yeast as a model. We exposed 180 populations of hybrids between species (Saccharomyces cerevisiae and Saccharomyces paradoxus) and their parental strains to UV mimetic and control conditions for approximately 100 generations. Although we found that adaptation occurs in both hybrids and parents, hybrids achieved a lower rate of adaptation, contrary to our expectations. Adaptation to DNA damage conditions comes with a large and similar cost for parents and hybrids, suggesting that this cost is not responsible for the lower adaptability of hybrids. We suggest that the lower adaptive potential of hybrids in this condition may result from the interaction between DNA damage and the inherent genetic instability of hybrids.
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Affiliation(s)
- Carla Bautista
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
- Département de Biochimie, de Microbiologie et de Bio‐informatiqueFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
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23
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Oliveira RKDM, Hurtado FA, Gomes PH, Puglia LL, Ferreira FF, Ranjan K, Albuquerque P, Poças-Fonseca MJ, Silva-Pereira I, Fernandes L. Base Excision Repair AP-Endonucleases-Like Genes Modulate DNA Damage Response and Virulence of the Human Pathogen Cryptococcus neoformans. J Fungi (Basel) 2021; 7:jof7020133. [PMID: 33673204 PMCID: PMC7917787 DOI: 10.3390/jof7020133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Pathogenic microbes are exposed to a number of potential DNA-damaging stimuli during interaction with the host immune system. Microbial survival in this situation depends on a fine balance between the maintenance of DNA integrity and the adaptability provided by mutations. In this study, we investigated the association of the DNA repair response with the virulence of Cryptococcus neoformans, a basidiomycete that causes life-threatening meningoencephalitis in immunocompromised individuals. We focused on the characterization of C. neoformansAPN1 and APN2 putative genes, aiming to evaluate a possible role of the predicted Apurinic/apyrimidinic (AP) endonucleases 1 and 2 of the base excision repair (BER) pathway on C. neoformans response to stress conditions and virulence. Our results demonstrated the involvement of the putative AP-endonucleases Apn1 and Apn2 in the cellular response to DNA damage induced by alkylation and by UV radiation, in melanin production, in tolerance to drugs and in virulence of C. neoformans in vivo. We also pointed out the potential use of DNA repair inhibitor methoxy-amine in combination with conventional antifungal drugs, for the development of new therapeutic approaches against this human fungal pathogen. This work provides new information about the DNA damage response of the highly important pathogenic fungus C. neoformans.
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Affiliation(s)
- Rayssa Karla de Medeiros Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Fabián Andrés Hurtado
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Pedro Henrique Gomes
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Luiza Lassi Puglia
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
| | - Fernanda Fonsêca Ferreira
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
| | - Kunal Ranjan
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
| | | | - Márcio José Poças-Fonseca
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (F.F.F.); (K.R.)
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
| | - Ildinete Silva-Pereira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília 70.910-900, Brazil; (R.K.d.M.O.); (F.A.H.); (P.H.G.); (L.L.P.)
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
| | - Larissa Fernandes
- Faculty of Ceilândia, University of Brasília, Brasília 72.220-275, Brazil;
- Correspondence: (M.J.P.-F.); (I.S.-P.); (L.F.)
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24
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Shin H, Park HR, Park JE, Yu SH, Yi G, Kim JH, Koh W, Kim HH, Lee SS, Huh JH. Reduced fertility caused by meiotic defects and micronuclei formation during microsporogenesis in xBrassicoraphanus. Genes Genomics 2021; 43:251-258. [PMID: 33555504 PMCID: PMC7966196 DOI: 10.1007/s13258-021-01050-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 01/12/2023]
Abstract
Background Hybridization and polyploidization events are important driving forces in plant evolution. Allopolyploids formed between different species can be naturally or artificially created but often suffer from genetic instability and infertility in successive generations. xBrassicoraphanus is an intergeneric allopolyploid obtained from a cross between Brassica rapa and Raphanus sativus, providing a useful resource for genetic and genomic study in hybrid species. Objective The current study aims to understand the cause of hybrid sterility and pollen abnormality in different lines of synthetic xBrassicoraphanus from the cytogenetic perspective. Methods Alexander staining was used to assess the pollen viability. Cytogenetic analysis was employed to monitor meiotic chromosome behaviors in pollen mother cells (PMCs). Origins of parental chromosomes in xBrassicoraphanus meiocytes were determined by genome in situ hybridization analysis. Results The xBrassicoraphanus lines BB#4 and BB#6 showed high rates of seed abortion and pollen deformation. Abnormal chromosome behaviors were observed in their PMCs, frequently forming univalents and inter-chromosomal bridges during meiosis. A positive correlation also exists between meiotic defects and the formation of micronuclei, which is conceivably responsible for unbalanced gamete production and pollen sterility. Conclusion These results suggest that unequal segregation of meiotic chromosomes, due in part to non-homologous interactions, is responsible for micronuclei and unbalanced gamete formation, eventually leading to pollen degeneration and inferior fertility in unstable xBrassicoraphanus lines.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Hye Rang Park
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Jeong Eun Park
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Seung Hwa Yu
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gibum Yi
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea
| | - Jung Hyo Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Wonjun Koh
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
| | | | - Jin Hoe Huh
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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25
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Mukaj A, Piálek J, Fotopulosova V, Morgan AP, Odenthal-Hesse L, Parvanov ED, Forejt J. Prdm9 Intersubspecific Interactions in Hybrid Male Sterility of House Mouse. Mol Biol Evol 2020; 37:3423-3438. [PMID: 32642764 PMCID: PMC7743643 DOI: 10.1093/molbev/msaa167] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
The classical definition posits hybrid sterility as a phenomenon when two parental taxa each of which is fertile produce a hybrid that is sterile. The first hybrid sterility gene in vertebrates, Prdm9, coding for a histone methyltransferase, was identified in crosses between two laboratory mouse strains derived from Mus mus musculus and M. m. domesticus subspecies. The unique function of PRDM9 protein in the initiation of meiotic recombination led to the discovery of the basic molecular mechanism of hybrid sterility in laboratory crosses. However, the role of this protein as a component of reproductive barrier outside the laboratory model remained unclear. Here, we show that the Prdm9 allelic incompatibilities represent the primary cause of reduced fertility in intersubspecific hybrids between M. m. musculus and M. m. domesticus including 16 musculus and domesticus wild-derived strains. Disruption of fertility phenotypes correlated with the rate of failure of synapsis between homologous chromosomes in meiosis I and with early meiotic arrest. All phenotypes were restored to normal when the domesticus Prdm9dom2 allele was substituted with the Prdm9dom2H humanized variant. To conclude, our data show for the first time the male infertility of wild-derived musculus and domesticus subspecies F1 hybrids controlled by Prdm9 as the major hybrid sterility gene. The impairment of fertility surrogates, testes weight and sperm count, correlated with increasing difficulties of meiotic synapsis of homologous chromosomes and with meiotic arrest, which we suppose reflect the increasing asymmetry of PRDM9-dependent DNA double-strand breaks.
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Affiliation(s)
- Amisa Mukaj
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vladana Fotopulosova
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | | | - Linda Odenthal-Hesse
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Emil D Parvanov
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jiri Forejt
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
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26
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Carleton KL, Conte MA, Malinsky M, Nandamuri SP, Sandkam BA, Meier JI, Mwaiko S, Seehausen O, Kocher TD. Movement of transposable elements contributes to cichlid diversity. Mol Ecol 2020; 29:4956-4969. [PMID: 33049090 DOI: 10.1111/mec.15685] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK.,Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | - Joana I Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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27
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Hénault M, Marsit S, Charron G, Landry CR. The effect of hybridization on transposable element accumulation in an undomesticated fungal species. eLife 2020; 9:e60474. [PMID: 32955438 PMCID: PMC7584455 DOI: 10.7554/elife.60474] [Citation(s) in RCA: 20] [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] [Received: 06/27/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can profoundly impact the evolution of genomes and species. A long-standing hypothesis suggests that hybridization could deregulate TEs and trigger their accumulation, although it received mixed support from studies mostly in plants and animals. Here, we tested this hypothesis in fungi using incipient species of the undomesticated yeast Saccharomyces paradoxus. Population genomic data revealed no signature of higher transposition in natural hybrids. As we could not rule out the elimination of past transposition increase signatures by natural selection, we performed a laboratory evolution experiment on a panel of artificial hybrids to measure TE accumulation in the near absence of selection. Changes in TE copy numbers were not predicted by the level of evolutionary divergence between the parents of a hybrid genotype. Rather, they were highly dependent on the individual hybrid genotypes, showing that strong genotype-specific deterministic factors govern TE accumulation in yeast hybrids.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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28
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Lucek K, Butlin RK, Patsiou T. Secondary contact zones of closely-related Erebia butterflies overlap with narrow phenotypic and parasitic clines. J Evol Biol 2020; 33:1152-1163. [PMID: 32573833 DOI: 10.1111/jeb.13669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Zones of secondary contact between closely related taxa are a common legacy of the Quaternary ice ages. Despite their abundance, the factors that keep species apart and prevent hybridization are often unknown. Here, we study a very narrow contact zone between three closely related butterfly species of the Erebia tyndarus species complex. Using genomic data, we first determined whether gene flow occurs and then assessed whether it might be hampered by differences in chromosome number between some species. We found interspecific gene flow between sibling species that differ in karyotype by one chromosome. Conversely, only F1 hybrids occurred between two species that have the same karyotype, forming a steep genomic cline. In a second step, we fitted clines to phenotypic, ecological and parasitic data to identify the factors associated with the genetic cline. We found clines for phenotypic data and the prevalence of the endosymbiont parasite Wolbachia to overlap with the genetic cline, suggesting that they might be drivers for separating the two species. Overall, our results highlight that some gene flow is possible between closely related species despite different chromosome numbers, but that other barriers restrict such gene flow.
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Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Theofania Patsiou
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Institute of Plant Sciences, Department of Biology, University of Bern, Bern, Switzerland
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de Vos JM, Augustijnen H, Bätscher L, Lucek K. Speciation through chromosomal fusion and fission in Lepidoptera. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190539. [PMID: 32654638 DOI: 10.1098/rstb.2019.0539] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera. Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jurriaan M de Vos
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Livio Bätscher
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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30
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Gabaldón T. Hybridization and the origin of new yeast lineages. FEMS Yeast Res 2020; 20:5870662. [PMID: 32658267 PMCID: PMC7394516 DOI: 10.1093/femsyr/foaa040] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
Hybrids originate from the mating of two diverged organisms, resulting in novel lineages that have chimeric genomes. Hybrids may exhibit unique phenotypic traits that are not necessarily intermediate between those present in the progenitors. These unique traits may enable them to thrive in new environments. Many hybrid lineages have been discovered among yeasts in the Saccharomycotina, of which many have industrial or clinical relevance, but this might reflect a bias toward investigating species with relevance to humans. Hybridization has also been proposed to be at the root of the whole-genome duplication in the lineage leading to Saccharomyces cerevisiae. Thus, hybridization seems to have played a prominent role in the evolution of Saccharomycotina yeasts, although it is still unclear how common this evolutionary process has been during the evolution of this and other fungal clades. Similarly, the evolutionary aftermath of hybridization, including implications at the genomic, transcriptional, physiological or ecological levels, remains poorly understood. In this review, I survey recent findings from genomic analysis of yeast hybrids of industrial or clinical relevance, and discuss the evolutionary implications of genomic hybridization for the origin of new lineages, including when such hybridization results in a whole-genome duplication.
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Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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31
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Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion‐Côté A. Using asexual vertebrates to study genome evolution and animal physiology: Banded ( Fundulus diaphanus) x Common Killifish ( F. heteroclitus) hybrid lineages as a model system. Evol Appl 2020; 13:1214-1239. [PMID: 32684956 PMCID: PMC7359844 DOI: 10.1111/eva.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/27/2022] Open
Abstract
Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.
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Affiliation(s)
| | - Svetlana Tirbhowan
- Department of BiologySaint Mary's UniversityHalifaxNSCanada
- Département de biologieUniversité de MonctonMonctonNBCanada
| | | | - Claude Power
- Département de biologieUniversité de MonctonMonctonNBCanada
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Park HR, Park JE, Kim JH, Shin H, Yu SH, Son S, Yi G, Lee SS, Kim HH, Huh JH. Meiotic Chromosome Stability and Suppression of Crossover Between Non-homologous Chromosomes in x Brassicoraphanus, an Intergeneric Allotetraploid Derived From a Cross Between Brassica rapa and Raphanus sativus. FRONTIERS IN PLANT SCIENCE 2020; 11:851. [PMID: 32612629 PMCID: PMC7309133 DOI: 10.3389/fpls.2020.00851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
Hybridization and polyploidization are major driving forces in plant evolution. Allopolyploids can be occasionally formed from a cross between distantly related species but often suffer from chromosome instability and infertility. xBrassicoraphanus is an intergeneric allotetraploid (AARR; 2n = 38) derived from a cross between Brassica rapa (AA; 2n = 20) and Raphanus sativus (RR; 2n = 18). xBrassicoraphanus is fertile and genetically stable, while retaining complete sets of both B. rapa and R. sativus chromosomes. Precise control of meiotic recombination is essential for the production of balanced gametes, and crossovers (COs) must occur exclusively between homologous chromosomes. Many interspecific hybrids have problems with meiotic division at early generations, in which interactions between non-homologous chromosomes often bring about aneuploidy and unbalanced gamete formation. We analyzed meiotic chromosome behaviors in pollen mother cells (PMCs) of allotetraploid and allodiploid F1 individuals of newly synthesized xBrassicoraphanus. Allotetraploid xBrassicoraphanus PMCs showed a normal diploid-like meiotic behavior. By contrast, allodiploid xBrassicoraphanus PMCs displayed abnormal segregation of chromosomes mainly due to the absence of homologous pairs. Notably, during early stages of meiosis I many of allodiploid xBrassicoraphanus chromosomes behave independently with few interactions between B. rapa and R. sativus chromosomes, forming many univalent chromosomes before segregation. Chromosomes were randomly assorted at later stages of meiosis, and tetrads with unequal numbers of chromosomes were formed at completion of meiosis. Immunolocalization of HEI10 protein mediating meiotic recombination revealed that COs were more frequent in synthetic allotetraploid xBrassicoraphanus than in allodiploid, but less than in the stabilized line. These findings suggest that structural dissimilarity between B. rapa and R. sativus chromosomes prevents non-homologous interactions between the parental chromosomes in allotetraploid xBrassicoraphanus, allowing normal diploid-like meiosis when homologous pairing partners are present. This study also suggests that CO suppression between non-homologous chromosomes is required for correct meiotic progression in newly synthesized allopolyploids, which is important for the formation of viable gametes and reproductive success in the hybrid progeny.
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Affiliation(s)
- Hye Rang Park
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Jung Hyo Kim
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Seung Hwa Yu
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Sehyeok Son
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Gibum Yi
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | | | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Abstract
Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.
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Affiliation(s)
- Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
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Sharma A, Kinney NA, Timoshevskiy VA, Sharakhova MV, Sharakhov IV. Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex. Genes (Basel) 2020; 11:E327. [PMID: 32204543 PMCID: PMC7140835 DOI: 10.3390/genes11030327] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, and An. quadriannulatus. Using fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA), a highly repetitive fraction of DNA, and heterochromatic Bacterial Artificial Chromosome (BAC) clones, we established the correspondence of pericentric heterochromatin between the metaphase and polytene X chromosomes of An. gambiae. We then developed chromosome idiograms and demonstrated that the X chromosomes exhibit qualitative differences in their pattern of heterochromatic bands and position of satellite DNA (satDNA) repeats among the sibling species with postzygotic isolation, An. arabiensis, An. merus, An. quadriannulatus, and An. coluzzii or An. gambiae. The identified differences in the size and structure of the X chromosome heterochromatin point to a possible role of repetitive DNA in speciation of mosquitoes. We found that An. coluzzii and An. gambiae, incipient species with prezygotic isolation, share variations in the relative positions of the satDNA repeats and the proximal heterochromatin band on the X chromosomes. This previously unknown genetic polymorphism in malaria mosquitoes may be caused by a differential amplification of DNA repeats or an inversion in the sex chromosome heterochromatin.
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Affiliation(s)
- Atashi Sharma
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
| | - Nicholas A. Kinney
- Genomics Bioinformatics and Computational Biology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA;
| | - Vladimir A. Timoshevskiy
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
| | - Maria V. Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 634050 Tomsk, Russia
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
- Genomics Bioinformatics and Computational Biology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA;
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Cytology and Genetics, Tomsk State University, 634050 Tomsk, Russia
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Morard M, Benavent-Gil Y, Ortiz-Tovar G, Pérez-Través L, Querol A, Toft C, Barrio E. Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity. Microb Genom 2020; 6:e000333. [PMID: 32065577 PMCID: PMC7200066 DOI: 10.1099/mgen.0.000333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/15/2020] [Indexed: 01/03/2023] Open
Abstract
Interspecific hybridization has played an important role in the evolution of eukaryotic organisms by favouring genetic interchange between divergent lineages to generate new phenotypic diversity involved in the adaptation to new environments. This way, hybridization between Saccharomyces species, involving the fusion between their metabolic capabilities, is a recurrent adaptive strategy in industrial environments. In the present study, whole-genome sequences of natural hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii were obtained to unveil the mechanisms involved in the origin and evolution of hybrids, as well as the ecological and geographic contexts in which spontaneous hybridization and hybrid persistence take place. Although Saccharomyces species can mate using different mechanisms, we concluded that rare-mating is the most commonly used, but other mechanisms were also observed in specific hybrids. The preponderance of rare-mating was confirmed by performing artificial hybridization experiments. The mechanism used to mate determines the genomic structure of the hybrid and its final evolutionary outcome. The evolution and adaptability of the hybrids are triggered by genomic instability, resulting in a wide diversity of genomic rearrangements. Some of these rearrangements could be adaptive under the stressful conditions of the industrial environment.
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Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Yaiza Benavent-Gil
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Guadalupe Ortiz-Tovar
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Centro de Estudios Vitivinícolas de Baja California, México, CETYS Universidad, Ensenada, Baja California, Mexico
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Institute for Integrative and Systems Biology, Universitat de València and CSIC, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
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Hemmer LW, Dias GB, Smith B, Van Vaerenberghe K, Howard A, Bergman CM, Blumenstiel JP. Hybrid dysgenesis in Drosophila virilis results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered. Mob DNA 2020; 11:10. [PMID: 32082426 PMCID: PMC7023781 DOI: 10.1186/s13100-020-0205-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are endogenous mutagens and their harmful effects are especially evident in syndromes of hybrid dysgenesis. In Drosophila virilis, hybrid dysgenesis is a syndrome of incomplete gonadal atrophy that occurs when males with multiple active TE families fertilize females that lack active copies of the same families. This has been demonstrated to cause the transposition of paternally inherited TE families, with gonadal atrophy driven by the death of germline stem cells. Because there are abundant, active TEs in the male inducer genome, that are not present in the female reactive genome, the D. virilis syndrome serves as an excellent model for understanding the effects of hybridization between individuals with asymmetric TE profiles. RESULTS Using the D. virilis syndrome of hybrid dysgenesis as a model, we sought to determine how the landscape of germline recombination is affected by parental TE asymmetry. Using a genotyping-by-sequencing approach, we generated a high-resolution genetic map of D. virilis and show that recombination rate and TE density are negatively correlated in this species. We then contrast recombination events in the germline of dysgenic versus non-dysgenic F1 females to show that the landscape of meiotic recombination is hardly perturbed during hybrid dysgenesis. In contrast, hybrid dysgenesis in the female germline increases transmission of chromosomes with mitotic recombination. Using a de novo PacBio assembly of the D. virilis inducer genome we show that clusters of mitotic recombination events in dysgenic females are associated with genomic regions with transposons implicated in hybrid dysgenesis. CONCLUSIONS Overall, we conclude that increased mitotic recombination is likely the result of early TE activation in dysgenic progeny, but a stable landscape of meiotic recombination indicates that either transposition is ameliorated in the adult female germline or that regulation of meiotic recombination is robust to ongoing transposition. These results indicate that the effects of parental TE asymmetry on recombination are likely sensitive to the timing of transposition.
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Affiliation(s)
- Lucas W. Hemmer
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045 USA
- Present Address: Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Guilherme B. Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 USA
| | - Brittny Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA
| | - Kelley Van Vaerenberghe
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045 USA
| | - Ashley Howard
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045 USA
| | - Casey M. Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 USA
| | - Justin P. Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045 USA
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37
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Fletcher NK, Acevedo P, Herman JS, Paupério J, Alves PC, Searle JB. Glacial cycles drive rapid divergence of cryptic field vole species. Ecol Evol 2019; 9:14101-14113. [PMID: 31938506 PMCID: PMC6953675 DOI: 10.1002/ece3.5846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 11/07/2022] Open
Abstract
Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single-nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise F ST values of 0.45-0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status.
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Affiliation(s)
| | - Pelayo Acevedo
- Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM‐CSIC‐JCCM)Ciudad RealSpain
| | - Jeremy S. Herman
- Department of Natural SciencesNational Museums ScotlandEdinburghUK
| | - Joana Paupério
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
| | - Paulo C. Alves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
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Lustyk D, Kinský S, Ullrich KK, Yancoskie M, Kašíková L, Gergelits V, Sedlacek R, Chan YF, Odenthal-Hesse L, Forejt J, Jansa P. Genomic Structure of Hstx2 Modifier of Prdm9-Dependent Hybrid Male Sterility in Mice. Genetics 2019; 213:1047-1063. [PMID: 31562180 PMCID: PMC6827376 DOI: 10.1534/genetics.119.302554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023] Open
Abstract
F1 hybrids between mouse inbred strains PWD and C57BL/6 represent the most thoroughly genetically defined model of hybrid sterility in vertebrates. Hybrid male sterility can be fully reconstituted from three components of this model, the Prdm9 gene, intersubspecific homeology of Mus musculus musculus and Mus musculus domesticus autosomes, and the X-linked Hstx2 locus. Hstx2 modulates the extent of Prdm9-dependent meiotic arrest and harbors two additional factors responsible for intersubspecific introgression-induced oligospermia (Hstx1) and meiotic recombination rate (Meir1). To facilitate positional cloning and to overcome the recombination suppression within the 4.3 Mb encompassing the Hstx2 locus, we designed Hstx2-CRISPR and SPO11/Cas9 transgenes aimed to induce DNA double-strand breaks specifically within the Hstx2 locus. The resulting recombinant reduced the Hstx2 locus to 2.70 Mb (chromosome X: 66.51-69.21 Mb). The newly defined Hstx2 locus still operates as the major X-linked factor of the F1 hybrid sterility, and controls meiotic chromosome synapsis and meiotic recombination rate. Despite extensive further crosses, the 2.70 Mb Hstx2 interval behaved as a recombination cold spot with reduced PRDM9-mediated H3K4me3 hotspots and absence of DMC1-defined DNA double-strand-break hotspots. To search for structural anomalies as a possible cause of recombination suppression, we used optical mapping and observed high incidence of subspecies-specific structural variants along the X chromosome, with a striking copy number polymorphism of the microRNA Mir465 cluster. This observation together with the absence of a strong sterility phenotype in Fmr1 neighbor (Fmr1nb) null mutants support the role of microRNA as a likely candidate for Hstx2.
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Affiliation(s)
- Diana Lustyk
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Faculty of Science, Charles University, Prague CZ-12000, Czech Republic
| | - Slavomír Kinský
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Kristian Karsten Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Michelle Yancoskie
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Lenka Kašíková
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Radislav Sedlacek
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Yingguang Frank Chan
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Petr Jansa
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
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Laporte M, Le Luyer J, Rougeux C, Dion-Côté AM, Krick M, Bernatchez L. DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species. SCIENCE ADVANCES 2019; 5:eaaw1644. [PMID: 31663013 PMCID: PMC6795504 DOI: 10.1126/sciadv.aaw1644] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 09/19/2019] [Indexed: 05/05/2023]
Abstract
The genomic shock hypothesis stipulates that the stress associated with divergent genome admixture can cause transposable element (TE) derepression, which could act as a postzygotic isolation mechanism. TEs affect gene structure, expression patterns, and chromosome organization and may have deleterious consequences when released. For these reasons, they are silenced by heterochromatin formation, which includes DNA methylation. Here, we show that a significant proportion of TEs are differentially methylated between the "dwarf" (limnetic) and the "normal" (benthic) whitefish, two nascent species that diverged some 15,000 generations ago within the Coregonus clupeaformis species complex. Moreover, TEs are overrepresented among loci that were demethylated in hybrids, indicative of their transcriptional derepression. These results are consistent with earlier studies in this system that revealed TE transcriptional derepression causes abnormal embryonic development and death of hybrids. Hence, this supports a role of DNA methylation reprogramming and TE derepression in postzygotic isolation of nascent animal species.
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Li N, Xu C, Zhang A, Lv R, Meng X, Lin X, Gong L, Wendel JF, Liu B. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. THE NEW PHYTOLOGIST 2019; 223:979-992. [PMID: 30919978 DOI: 10.1111/nph.15820] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/21/2019] [Indexed: 05/18/2023]
Abstract
Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.
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Affiliation(s)
- Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol 2019; 28:1491-1505. [DOI: 10.1111/mec.14969] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Stefan Dennenmoser
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
| | | | - Michael C. Schatz
- Cold Spring Harbor Laboratory Cold Spring Harbor New York
- Departments of Computer Science and Biology Johns Hopkins University Baltimore Maryland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human Genetics University of Cologne Cologne Germany
| | | | - Arne W. Nolte
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
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Puerma E, Orengo DJ, Cruz F, Gómez-Garrido J, Librado P, Salguero D, Papaceit M, Gut M, Segarra C, Alioto TS, Aguadé M. The High-Quality Genome Sequence of the Oceanic Island Endemic Species Drosophila guanche Reveals Signals of Adaptive Evolution in Genes Related to Flight and Genome Stability. Genome Biol Evol 2018; 10:1956-1969. [PMID: 29947749 PMCID: PMC6101566 DOI: 10.1093/gbe/evy135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/18/2022] Open
Abstract
Drosophila guanche is a member of the obscura group that originated in the Canary Islands archipelago upon its colonization by D. subobscura. It evolved into a new species in the laurisilva, a laurel forest present in wet regions that in the islands have only minor long-term weather fluctuations. Oceanic island endemic species such as D. guanche can become model species to investigate not only the relative role of drift and adaptation in speciation processes but also how population size affects nucleotide variation. Moreover, the previous identification of two satellite DNAs in D. guanche makes this species attractive for studying how centromeric DNA evolves. As a prerequisite for its establishment as a model species suitable to address all these questions, we generated a high-quality D. guanche genome sequence composed of 42 cytologically mapped scaffolds, which are assembled into six super-scaffolds (one per chromosome). The comparative analysis of the D. guanche proteome with that of twelve other Drosophila species identified 151 genes that were subject to adaptive evolution in the D. guanche lineage, with a subset of them being involved in flight and genome stability. For example, the Centromere Identifier (CID) protein, directly interacting with centromeric satellite DNA, shows signals of adaptation in this species. Both genomic analyses and FISH of the two satellites would support an ongoing replacement of centromeric satellite DNA in D. guanche.
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Affiliation(s)
- Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, France
| | - David Salguero
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Montserrat Papaceit
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen Segarra
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Tyler S Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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Seixas FA, Boursot P, Melo-Ferreira J. The genomic impact of historical hybridization with massive mitochondrial DNA introgression. Genome Biol 2018; 19:91. [PMID: 30056805 PMCID: PMC6065068 DOI: 10.1186/s13059-018-1471-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. RESULTS Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. CONCLUSIONS General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
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Affiliation(s)
- Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France.
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
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Evolutionary Mechanisms of Varying Chromosome Numbers in the Radiation of Erebia Butterflies. Genes (Basel) 2018; 9:genes9030166. [PMID: 29547586 PMCID: PMC5867887 DOI: 10.3390/genes9030166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 02/03/2023] Open
Abstract
The evolution of intrinsic barriers to gene flow is a crucial step in the process of speciation. Chromosomal changes caused by fusion and fission events are one such barrier and are common in several groups of Lepidoptera. However, it remains unclear if and how chromosomal changes have contributed to speciation in this group. I tested for a phylogenetic signal of varying chromosome numbers in Erebia butterflies by combining existing sequence data with karyological information. I also compared different models of trait evolution in order to infer the underlying evolutionary mechanisms. Overall, I found significant phylogenetic signals that are consistent with non-neutral trait evolution only when parts of the mitochondrial genome were included, suggesting cytonuclear discordances. The adaptive evolutionary model tested in this study consistently outperformed the neutral model of trait evolution. Taken together, these results suggest that, unlike other Lepidoptera groups, changes in chromosome numbers may have played a role in the diversification of Erebia butterflies.
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Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Curr Opin Genet Dev 2018; 49:15-24. [PMID: 29505963 DOI: 10.1016/j.gde.2018.02.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/30/2022]
Abstract
It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated. To support this proposal, we compile a list of examples, including some previously unrecognized, whereby new host functions and phenotypes can be directly attributed to horizontally acquired TE or viral sequences. We predict that the number of examples will rapidly grow in the future as the prevalence of horizontal transfer in the life cycle of TEs becomes even more apparent, firmly establishing this form of non-Mendelian inheritance as a consequential facet of eukaryotic evolution.
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Ren X, Li R, Wei X, Bi Y, Ho V, Ding Q, Xu Z, Zhang Z, Hsieh CL, Young A, Zeng J, Liu X, Zhao Z. Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni. Nucleic Acids Res 2018; 46:1295-1307. [PMID: 29325078 PMCID: PMC5814819 DOI: 10.1093/nar/gkx1277] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/07/2017] [Accepted: 12/19/2017] [Indexed: 02/06/2023] Open
Abstract
DNA recombination is required for effective segregation and diversification of genomes and for the successful completion of meiosis. Recent studies in various species hybrids have demonstrated a genetic link between DNA recombination and speciation. Consistent with this, we observed a striking suppression of recombination in the hybrids between two nematodes, the hermaphroditic Caenorhabditis briggsae and the gonochoristic C. nigoni. To unravel the molecular basis underlying the recombination suppression in their hybrids, we generated a C. nigoni genome with chromosome-level contiguity and produced an improved C. briggsae genome with resolved gaps up to 2.8 Mb. The genome alignment reveals not only high sequence divergences but also pervasive intra- and inter-chromosomal sequence re-arrangements between the two species, which are plausible culprits for the observed suppression. Comparison of recombination boundary sequences suggests that recombination in the hybrid requires extensive sequence homology, which is rarely seen between the two genomes. The new genomes and genomic libraries form invaluable resources for studying genome evolution, hybrid incompatibilities and sex evolution for this pair of model species.
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Affiliation(s)
- Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaolin Wei
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Bi
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhichao Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhihong Zhang
- Illumina Inc., 5200 Illumina Way, San Diego 92122, USA
| | | | - Amanda Young
- Illumina Inc., 5200 Illumina Way, San Diego 92122, USA
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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