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Kotari I, Kosiol C, Borges R. The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases. Mol Biol Evol 2024; 41:msae080. [PMID: 38667829 PMCID: PMC11108087 DOI: 10.1093/molbev/msae080] [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: 05/05/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Different frequencies amongst codons that encode the same amino acid (i.e. synonymous codons) have been observed in multiple species. Studies focused on uncovering the forces that drive such codon usage showed that a combined effect of mutational biases and translational selection works to produce different frequencies of synonymous codons. However, only few have been able to measure and distinguish between these forces that may leave similar traces on the coding regions. Here, we have developed a codon model that allows the disentangling of mutation, selection on amino acids and synonymous codons, and GC-biased gene conversion (gBGC) which we employed on an extensive dataset of 415 chordates and 191 arthropods. We found that chordates need 15 more synonymous codon categories than arthropods to explain the empirical codon frequencies, which suggests that the extent of codon usage can vary greatly between animal phyla. Moreover, methylation at CpG sites seems to partially explain these patterns of codon usage in chordates but not in arthropods. Despite the differences between the two phyla, our findings demonstrate that in both, GC-rich codons are disfavored when mutations are GC-biased, and the opposite is true when mutations are AT-biased. This indicates that selection on the genomic coding regions might act primarily to stabilize its GC/AT content on a genome-wide level. Our study shows that the degree of synonymous codon usage varies considerably among animals, but is likely governed by a common underlying dynamic.
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Affiliation(s)
- Ioanna Kotari
- Institut für Populationsgenetik, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Carolin Kosiol
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife KY16 9TH, UK
| | - Rui Borges
- Institut für Populationsgenetik, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
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2
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Kyriacou RG, Mulhair PO, Holland PWH. GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences. J Mol Evol 2024; 92:138-152. [PMID: 38491221 PMCID: PMC10978632 DOI: 10.1007/s00239-024-10160-5] [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: 09/13/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Diptera, Coleoptera and Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.
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Affiliation(s)
- Riccardo G Kyriacou
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter O Mulhair
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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3
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Liu Y, Liang N, Xian Q, Zhang W. GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2. BMC PLANT BIOLOGY 2023; 23:608. [PMID: 38036992 PMCID: PMC10691020 DOI: 10.1186/s12870-023-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/26/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Despite GC variation constitutes a fundamental element of genome and species diversity, the precise mechanisms driving it remain unclear. The abundant sequence data available for the ITS2, a commonly employed phylogenetic marker in plants, offers an exceptional resource for exploring the GC variation across angiosperms. RESULTS A comprehensive selection of 8666 species, comprising 165 genera, 63 families, and 30 orders were used for the analyses. The alignment of ITS2 sequence-structures and partitioning of secondary structures into paired and unpaired regions were performed using 4SALE. Substitution rates and frequencies among GC base-pairs in the paired regions of ITS2 were calculated using RNA-specific models in the PHASE package. The results showed that the distribution of ITS2 GC contents on the angiosperm phylogeny was heterogeneous, but their increase was generally associated with ITS2 sequence homogenization, thereby supporting the occurrence of GC-biased gene conversion (gBGC) during the concerted evolution of ITS2. Additionally, the GC content in the paired regions of the ITS2 secondary structure was significantly higher than that of the unpaired regions, indicating the selection of GC for thermodynamic stability. Furthermore, the RNA substitution models demonstrated that base-pair transformations favored both the elevation and fixation of GC in the paired regions, providing further support for gBGC. CONCLUSIONS Our findings highlight the significance of secondary structure in GC investigation, which demonstrate that both gBGC and structure-based selection are influential factors driving angiosperm ITS2 GC content.
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Affiliation(s)
- Yubo Liu
- Marine College, Shandong University, Weihai, 264209, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Nan Liang
- Marine College, Shandong University, Weihai, 264209, China
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qing Xian
- Marine College, Shandong University, Weihai, 264209, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, 264209, China.
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Bourret J, Borvető F, Bravo IG. Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: The showcase of polypyrimidine tract binding proteins. J Evol Biol 2023; 36:1375-1392. [PMID: 37667674 DOI: 10.1111/jeb.14212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 09/06/2023]
Abstract
Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel functions. Here, we focused our study on gene paralogs on the evolutionary history of the three polypyrimidine tract binding protein genes (PTBP) and their concurrent evolution of differential codon usage preferences (CUPrefs) in vertebrate species. PTBP1-3 show high identity at the amino acid level (up to 80%) but display strongly different nucleotide composition, divergent CUPrefs and, in humans and in many other vertebrates, distinct tissue-specific expression levels. Our phylogenetic inference results show that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates, and genomic context analysis illustrates that local synteny has been well preserved over time for the three paralogs. We identify a distinct evolutionary pattern towards GC3-enriching substitutions in PTBP1, concurrent with enrichment in frequently used codons and with a tissue-wide expression. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. As a result of this substitution trend, CUPrefs sharply differ between mammalian PTBP1s and the rest of PTBPs. Genomic context analysis suggests that GC3-rich nucleotide composition in PTBP1s is driven by local substitution processes, while the evidence in this direction is thinner for PTBP2-3. An actual lack of co-variation between the observed GC composition of PTBP2-3 and that of the surrounding non-coding genomic environment would raise an interrogation on the origin of CUPrefs, warranting further research on a putative tissue-specific translational selection. Finally, we communicate an intriguing trend for the use of the UUG-Leu codon, which matches the trends of AT-ending codons. Our results are compatible with a scenario in which a combination of directional mutation-selection processes would have differentially shaped CUPrefs of PTBPs in vertebrates: the observed GC-enrichment of PTBP1 in placental mammals may be linked to genomic location and to the strong and broad tissue-expression, while AT-enrichment of PTBP2 and PTBP3 would be associated with rare CUPrefs and thus, possibly to specialized spatio-temporal expression. Our interpretation is coherent with a gene subfunctionalisation process by differential expression regulation associated with the evolution of specific CUPrefs.
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Affiliation(s)
- Jérôme Bourret
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Fanni Borvető
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
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5
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Näsvall K, Boman J, Talla V, Backström N. Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies. Genome Biol Evol 2023; 15:evad150. [PMID: 37565492 PMCID: PMC10462419 DOI: 10.1093/gbe/evad150] [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: 11/22/2022] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage.
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Affiliation(s)
- Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Venkat Talla
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
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6
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Fu Y, Liang F, Li C, Warren A, Shin MK, Li L. Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa. Microorganisms 2023; 11:1833. [PMID: 37513005 PMCID: PMC10384029 DOI: 10.3390/microorganisms11071833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.
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Affiliation(s)
- Yu Fu
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Fasheng Liang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Congjun Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Mann Kyoon Shin
- Department of Biology, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
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7
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Komluski J, Habig M, Stukenbrock EH. Repeat-Induced Point Mutation and Gene Conversion Coinciding with Heterochromatin Shape the Genome of a Plant-Pathogenic Fungus. mBio 2023:e0329022. [PMID: 37093087 DOI: 10.1128/mbio.03290-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Meiosis is associated with genetic changes in the genome-via recombination, gene conversion, and mutations. The occurrence of gene conversion and mutations during meiosis may further be influenced by the chromatin conformation, similar to the effect of the chromatin conformation on the mitotic mutation rate. To date, however, the exact distribution and type of meiosis-associated changes and the role of the chromatin conformation in this context are largely unexplored. Here, we determine recombination, gene conversion, and de novo mutations using whole-genome sequencing of all meiotic products of 23 individual meioses in Zymoseptoria tritici, an important pathogen of wheat. We confirm a high genome-wide recombination rate of 65 centimorgan (cM)/Mb and see higher recombination rates on the accessory compared to core chromosomes. A substantial fraction of 0.16% of all polymorphic markers was affected by gene conversions, showing a weak GC-bias and occurring at higher frequency in regions of constitutive heterochromatin, indicated by the histone modification H3K9me3. The de novo mutation rate associated with meiosis was approximately three orders of magnitude higher than the corresponding mitotic mutation rate. Importantly, repeat-induced point mutation (RIP), a fungal defense mechanism against duplicated sequences, is active in Z. tritici and responsible for the majority of these de novo meiotic mutations. Our results indicate that the genetic changes associated with meiosis are a major source of variability in the genome of an important plant pathogen and shape its evolutionary trajectory. IMPORTANCE The impact of meiosis on the genome composition via gene conversion and mutations is mostly poorly understood, in particular, for non-model species. Here, we sequenced all four meiotic products for 23 individual meioses and determined the genetic changes caused by meiosis for the important fungal wheat pathogen Zymoseptoria tritici. We found a high rate of gene conversions and an effect of the chromatin conformation on gene conversion rates. Higher conversion rates were found in regions enriched with the H3K9me3-a mark for constitutive heterochromatin. Most importantly, meiosis was associated with a much higher frequency of de novo mutations than mitosis; 78% of the meiotic mutations were caused by repeat-induced point mutations-a fungal defense mechanism against duplicated sequences. In conclusion, the genetic changes associated with meiosis are therefore a major factor shaping the genome of this fungal pathogen.
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Affiliation(s)
- Jovan Komluski
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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8
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Xian Q, Wang S, Liu Y, Kan S, Zhang W. Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species. Int J Mol Sci 2023; 24:ijms24097716. [PMID: 37175423 PMCID: PMC10178233 DOI: 10.3390/ijms24097716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 Corydalis species, and their GC contents were comparatively investigated in the context of ITS2's characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2's concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content.
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Affiliation(s)
- Qing Xian
- Marine College, Shandong University, Weihai 264209, China
| | - Suyin Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Yanyan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai 264209, China
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9
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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10
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Vozárová R, Wang W, Lunerová J, Shao F, Pellicer J, Leitch IJ, Leitch AR, Kovařík A. Mega-sized pericentromeric blocks of simple telomeric repeats and their variants reveal patterns of chromosome evolution in ancient Cycadales genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:646-663. [PMID: 36065632 PMCID: PMC9827991 DOI: 10.1111/tpj.15969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/19/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000-fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non-telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase-sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant-specific probes revealed canonical Arabidopsis-type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads.
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Affiliation(s)
- Radka Vozárová
- Department of Molecular EpigeneticsInstitute of Biophysics, Czech Academy of Sciencesv.v.i., Královopolská 135612 65BrnoCzech Republic
- Department of Experimental Biology, Faculty of ScienceMasaryk University611 37BrnoCzech Republic
| | - Wencai Wang
- Science and Technology Innovation CentreGuangzhou University of Chinese MedicineGuangzhou510405China
| | - Jana Lunerová
- Department of Molecular EpigeneticsInstitute of Biophysics, Czech Academy of Sciencesv.v.i., Královopolská 135612 65BrnoCzech Republic
| | - Fengqing Shao
- Science and Technology Innovation CentreGuangzhou University of Chinese MedicineGuangzhou510405China
| | - Jaume Pellicer
- Royal Botanic GardensKew, RichmondSurreyTW9 3ABUK
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia sn08038BarcelonaSpain
| | | | - Andrew R. Leitch
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
| | - Aleš Kovařík
- Department of Molecular EpigeneticsInstitute of Biophysics, Czech Academy of Sciencesv.v.i., Královopolská 135612 65BrnoCzech Republic
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11
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Poszewiecka B, Gogolewski K, Stankiewicz P, Gambin A. Revised time estimation of the ancestral human chromosome 2 fusion. BMC Genomics 2022; 23:616. [PMID: 36008753 PMCID: PMC9413910 DOI: 10.1186/s12864-022-08828-7] [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: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
Background The reduction of the chromosome number from 48 in the Great Apes to 46 in modern humans is thought to result from the end-to-end fusion of two ancestral non-human primate chromosomes forming the human chromosome 2 (HSA2). Genomic signatures of this event are the presence of inverted telomeric repeats at the HSA2 fusion site and a block of degenerate satellite sequences that mark the remnants of the ancestral centromere. It has been estimated that this fusion arose up to 4.5 million years ago (Mya). Results We have developed an enhanced algorithm for the detection and efficient counting of the locally over-represented weak-to-strong (AT to GC) substitutions. By analyzing the enrichment of these substitutions around the fusion site of HSA2 we estimated its formation time at 0.9 Mya with a 95% confidence interval of 0.4-1.5 Mya. Additionally, based on the statistics derived from our algorithm, we have reconstructed the evolutionary distances among the Great Apes (Hominoidea). Conclusions Our results shed light on the HSA2 fusion formation and provide a novel computational alternative for the estimation of the speciation chronology.
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Affiliation(s)
| | | | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, US
| | - Anna Gambin
- Institute of Informatics, Warsaw University, Warsaw, Poland
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Berdan EL, Blanckaert A, Butlin RK, Flatt T, Slotte T, Wielstra B. Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210199. [PMID: 35694750 PMCID: PMC9189497 DOI: 10.1098/rstb.2021.0199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/24/2022] [Indexed: 12/26/2022] Open
Abstract
Supergenes offer spectacular examples of long-term balancing selection in nature, but their origin and maintenance remain a mystery. Reduced recombination between arrangements, a critical aspect of many supergenes, protects adaptive multi-trait phenotypes but can lead to mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One outcome is the formation of maladaptive balanced lethal systems, where only heterozygotes remain viable and reproduce. We investigated the conditions under which these different outcomes occur, assuming a scenario of introgression after divergence. We found that AOD aided the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism was easily destabilized by further mutation accumulation, which was often asymmetric, disrupting the quasi-equilibrium state. Mechanisms that accelerated degeneration tended to amplify asymmetric mutation accumulation between the supergene arrangements and vice-versa. As the evolution of balanced lethal systems requires symmetric degeneration of both arrangements, this leaves only restricted conditions for their evolution, namely small population sizes and low rates of gene conversion. The dichotomy between the persistence of polymorphism and degeneration of supergene arrangements likely underlies the rarity of balanced lethal systems in nature. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Emma L. Berdan
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
- Tjarnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Stromstad, Sweden
| | - Alexandre Blanckaert
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Roger K. Butlin
- Tjarnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Stromstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Ben Wielstra
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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13
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Li M, Sun C, Xu N, Bian P, Tian X, Wang X, Wang Y, Jia X, Heller R, Wang M, Wang F, Dai X, Luo R, Guo Y, Wang X, Yang P, Hu D, Liu Z, Fu W, Zhang S, Li X, Wen C, Lan F, Siddiki AZ, Suwannapoom C, Zhao X, Nie Q, Hu X, Jiang Y, Yang N. De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions. Mol Biol Evol 2022; 39:msac066. [PMID: 35325213 PMCID: PMC9021737 DOI: 10.1093/molbev/msac066] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaomeng Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China
| | - Xinzheng Jia
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Mingshan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Rongsong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiangnan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhenyu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shunjin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Fangren Lan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University, Chittagong 4202, Bangladesh
| | | | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, QC, Canada
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
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14
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Carpentier F, Rodríguez de la Vega RC, Jay P, Duhamel M, Shykoff JA, Perlin MH, Wallen RM, Hood ME, Giraud T. Tempo of degeneration across independently evolved non-recombining regions. Mol Biol Evol 2022; 39:6553583. [PMID: 35325190 PMCID: PMC9004411 DOI: 10.1093/molbev/msac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression can evolve and lead to genomic degeneration, in particular on sex chromosomes. Here, we investigated the tempo of degeneration in nonrecombining regions, that is, the function curve for the accumulation of deleterious mutations over time, leveraging on 22 independent events of recombination suppression identified on mating-type chromosomes of anther-smut fungi, including newly identified ones. Using previously available and newly generated high-quality genome assemblies of alternative mating types of 13 Microbotryum species, we estimated degeneration levels in terms of accumulation of nonoptimal codons and nonsynonymous substitutions in nonrecombining regions. We found a reduced frequency of optimal codons in the nonrecombining regions compared with autosomes, that was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared with recombining regions. The frequency of optimal codons rapidly decreased following recombination suppression and reached an asymptote after ca. 3 Ma. The strength of purifying selection remained virtually constant at dN/dS = 0.55, that is, at an intermediate level between purifying selection and neutral evolution. Accordingly, nonsynonymous differences between mating-type chromosomes increased linearly with stratum age, at a rate of 0.015 per My. We thus develop a method for disentangling effects of reduced selection efficacy from GC-biased gene conversion in the evolution of codon usage and we quantify the tempo of degeneration in nonrecombining regions, which is important for our knowledge on genomic evolution and on the maintenance of regions without recombination.
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Affiliation(s)
- Fantin Carpentier
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Université de Lille, CNRS, UMR 8198-Evo-Eco-Paleo F-59000, Lille, France
| | - Ricardo C. Rodríguez de la Vega
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
| | - Paul Jay
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Marine Duhamel
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jacqui A. Shykoff
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Michael H. Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | - R. Margaret Wallen
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | | | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
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15
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Pettie N, Llopart A, Comeron JM. Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba. PLoS Genet 2022; 18:e1010087. [PMID: 35320272 PMCID: PMC8979470 DOI: 10.1371/journal.pgen.1010087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 04/04/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
The number and location of crossovers across genomes are highly regulated during meiosis, yet the key components controlling them are fast evolving, hindering our understanding of the mechanistic causes and evolutionary consequences of changes in crossover rates. Drosophila melanogaster has been a model species to study meiosis for more than a century, with an available high-resolution crossover map that is, nonetheless, missing for closely related species, thus preventing evolutionary context. Here, we applied a novel and highly efficient approach to generate whole-genome high-resolution crossover maps in D. yakuba to tackle multiple questions that benefit from being addressed collectively within an appropriate phylogenetic framework, in our case the D. melanogaster species subgroup. The genotyping of more than 1,600 individual meiotic events allowed us to identify several key distinct properties relative to D. melanogaster. We show that D. yakuba, in addition to higher crossover rates than D. melanogaster, has a stronger centromere effect and crossover assurance than any Drosophila species analyzed to date. We also report the presence of an active crossover-associated meiotic drive mechanism for the X chromosome that results in the preferential inclusion in oocytes of chromatids with crossovers. Our evolutionary and genomic analyses suggest that the genome-wide landscape of crossover rates in D. yakuba has been fairly stable and captures a significant signal of the ancestral crossover landscape for the whole D. melanogaster subgroup, even informative for the D. melanogaster lineage. Contemporary crossover rates in D. melanogaster, on the other hand, do not recapitulate ancestral crossovers landscapes. As a result, the temporal stability of crossover landscapes observed in D. yakuba makes this species an ideal system for applying population genetic models of selection and linkage, given that these models assume temporal constancy in linkage effects. Our studies emphasize the importance of generating multiple high-resolution crossover rate maps within a coherent phylogenetic context to broaden our understanding of crossover control during meiosis and to improve studies on the evolutionary consequences of variable crossover rates across genomes and time.
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Affiliation(s)
- Nikale Pettie
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Ana Llopart
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Josep M. Comeron
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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16
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Wint R, Salamov A, Grigoriev IV. Kingdom-Wide Analysis of Fungal Transcriptomes and tRNAs Reveals Conserved Patterns of Adaptive Evolution. Mol Biol Evol 2022; 39:6513383. [PMID: 35060603 PMCID: PMC8826637 DOI: 10.1093/molbev/msab372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.
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Affiliation(s)
- Rhondene Wint
- Molecular and Cell Biology Unit, Quantitative and Systems Biology Program, University of California Merced, Merced, CA, 95343, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720 US
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17
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Bonito M, D’Atanasio E, Ravasini F, Cariati S, Finocchio A, Novelletto A, Trombetta B, Cruciani F. New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion. Hum Mol Genet 2021; 30:2272-2285. [PMID: 34244762 PMCID: PMC8600007 DOI: 10.1093/hmg/ddab189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
About one-quarter of the euchromatic portion of the male-specific region of the human Y chromosome consists of large duplicated sequences that are organized in eight palindromes (termed P1-P8), which undergo arm-to arm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although the relevance of gene conversion in the evolution of palindromic sequences has been profoundly recognized, the dynamic of this mechanism is still nuanced. To shed light into the evolution of these genomic elements, we performed a high-depth (50×) targeted next-generation sequencing of the palindrome P6 in 157 subjects belonging to the most divergent evolutionary lineages of the Y chromosome. We found 118 new paralogous sequence variants, which were placed into the context of a robust Y chromosome phylogeny based on 7240 SNPs of the X-degenerate region. We mapped along the phylogeny 80 gene conversion events that shaped the diversity of P6 arms during recent human history. In contrast to previous studies, we demonstrated that arm-to-arm gene conversion, which occurs at a rate of 6.01 × 10 -6 conversions/base/year, is not biased toward the retention of the ancestral state of sequences. We also found a significantly lower mutation rate of the arms (6.18 × 10-10 mutations/base/year) compared with the spacer (9.16 × 10-10 mutations/base/year), a finding that may explain the observed higher inter-species conservation of arms, without invoking any bias of conversion. Finally, by formally testing the mutation/conversion balance in P6, we found that the arms of this palindrome reached a steady-state equilibrium between mutation and gene conversion.
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Affiliation(s)
- Maria Bonito
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 0185, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Selene Cariati
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Andrea Finocchio
- Department of Biology, University of Rome Tor Vergata, Rome 0133, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome 0133, Italy
| | - Beniamino Trombetta
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 0185, Italy
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18
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Jackson EK, Bellott DW, Skaletsky H, Page DC. GC-biased gene conversion in X-chromosome palindromes conserved in human, chimpanzee, and rhesus macaque. G3 GENES|GENOMES|GENETICS 2021; 11:6317831. [PMID: 34849781 PMCID: PMC8981503 DOI: 10.1093/g3journal/jkab224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022]
Abstract
Gene conversion is GC-biased across a wide range of taxa. Large palindromes on mammalian
sex chromosomes undergo frequent gene conversion that maintains arm-to-arm sequence
identity greater than 99%, which may increase their susceptibility to the effects of
GC-biased gene conversion. Here, we demonstrate a striking history of GC-biased gene
conversion in 12 palindromes conserved on the X chromosomes of human, chimpanzee, and
rhesus macaque. Primate X-chromosome palindrome arms have significantly higher GC content
than flanking single-copy sequences. Nucleotide replacements that occurred in human and
chimpanzee palindrome arms over the past 7 million years are one-and-a-half times as
GC-rich as the ancestral bases they replaced. Using simulations, we show that our observed
pattern of nucleotide replacements is consistent with GC-biased gene conversion with a
magnitude of 70%, similar to previously reported values based on analyses of human
meioses. However, GC-biased gene conversion since the divergence of human and rhesus
macaque explains only a fraction of the observed difference in GC content between
palindrome arms and flanking sequence, suggesting that palindromes are older than 29
million years and/or had elevated GC content at the time of their formation. This work
supports a greater than 2:1 preference for GC bases over AT bases during gene conversion
and demonstrates that the evolution and composition of mammalian sex chromosome
palindromes is strongly influenced by GC-biased gene conversion.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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19
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Hong Y, Zhang D, Zhou X, Chen A, Abliz A, Bai J, Wang L, Hu Q, Gong K, Guan X, Liu M, Zheng X, Lai S, Qu H, Zhao F, Hao S, Wu Z, Cai H, Hu S, Ma Y, Zhang J, Ke Y, Wang QF, Chen W, Zeng C. Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:177-191. [PMID: 34624550 PMCID: PMC9510933 DOI: 10.1016/j.gpb.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 12/04/2022]
Abstract
Postzygotic mutations are acquired in normal tissues throughout an individual’s lifetime and hold clues for identifying mutagenic factors. Here, we investigated postzygotic mutation spectra of healthy individuals using optimized ultra-deep exome sequencing of the time-series samples from the same volunteer as well as the samples from different individuals. In blood, sperm, and muscle cells, we resolved three common types of mutational signatures. Signatures A and B represent clock-like mutational processes, and the polymorphisms of epigenetic regulation genes influence the proportion of signature B in mutation profiles. Notably, signature C, characterized by C>T transitions at GpCpN sites, tends to be a feature of diverse normal tissues. Mutations of this type are likely to occur early during embryonic development, supported by their relatively high allelic frequencies, presence in multiple tissues, and decrease in occurrence with age. Almost none of the public datasets for tumors feature this signature, except for 19.6% of samples of clear cell renal cell carcinoma with increased activation of the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Moreover, the accumulation of signature C in the mutation profile was accelerated in a human embryonic stem cell line with drug-induced activation of HIF-1α. Thus, embryonic hypoxia may explain this novel signature across multiple normal tissues. Our study suggests that hypoxic condition in an early stage of embryonic development is a crucial factor inducing C>T transitions at GpCpN sites; and individuals’ genetic background may also influence their postzygotic mutation profiles.
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Affiliation(s)
- Yaqiang Hong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dake Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xiangtian Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325035, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou 325035, China
| | - Aili Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Amir Abliz
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Liang Wang
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Qingtao Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Kenan Gong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Xiaonan Guan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Mengfei Liu
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinchang Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujuan Lai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Fuxin Zhao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325035, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou 325035, China
| | - Shuang Hao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhen Wu
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Hong Cai
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Yue Ma
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junting Zhang
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qian-Fei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Collaborative Innovation Center for Genetics and Development, Shanghai 200438, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Brandt A, Tran Van P, Bluhm C, Anselmetti Y, Dumas Z, Figuet E, François CM, Galtier N, Heimburger B, Jaron KS, Labédan M, Maraun M, Parker DJ, Robinson-Rechavi M, Schaefer I, Simion P, Scheu S, Schwander T, Bast J. Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova. Proc Natl Acad Sci U S A 2021; 118:e2101485118. [PMID: 34535550 PMCID: PMC8463897 DOI: 10.1073/pnas.2101485118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/05/2022] Open
Abstract
Sex strongly impacts genome evolution via recombination and segregation. In the absence of these processes, haplotypes within lineages of diploid organisms are predicted to accumulate mutations independently of each other and diverge over time. This so-called "Meselson effect" is regarded as a strong indicator of the long-term evolution under obligate asexuality. Here, we present genomic and transcriptomic data of three populations of the asexual oribatid mite species Oppiella nova and its sexual relative Oppiella subpectinata We document strikingly different patterns of haplotype divergence between the two species, strongly supporting Meselson effect-like evolution and long-term asexuality in O. nova: I) variation within individuals exceeds variation between populations in O. nova but vice versa in O. subpectinata; II) two O. nova sublineages feature a high proportion of lineage-specific heterozygous single-nucleotide polymorphisms (SNPs), indicating that haplotypes continued to diverge after lineage separation; III) the deepest split in gene trees generally separates the two haplotypes in O. nova, but populations in O. subpectinata; and IV) the topologies of the two haplotype trees match each other. Our findings provide positive evidence for the absence of canonical sex over evolutionary time in O. nova and suggest that asexual oribatid mites can escape the dead-end fate usually associated with asexual lineages.
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Affiliation(s)
- Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany;
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Bluhm
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
- Abteilung Boden und Umwelt, Forstliche Versuchs- und Forschungsanstalt Baden-Wuerttemberg, 79100 Freiburg, Germany
| | - Yoann Anselmetti
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- CoBIUS Lab, Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Emeric Figuet
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
| | - Clémentine M François
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, École Nationale des Travaux Publics de l'État, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
| | - Nicolas Galtier
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
| | - Bastian Heimburger
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Marjorie Labédan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mark Maraun
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ina Schaefer
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Paul Simion
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- Laboratory of Evolutionary Genetics and Ecology, Unit in Environmental and Evolutionary Biology, Université de Namur, 5000 Namur, Belgium
| | - Stefan Scheu
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
- Section Biodiversity and Ecology, Centre of Biodiversity and Sustainable Land Use, 37073 Goettingen, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Institute for Zoology, University of Cologne, 50674 Cologne, Germany
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21
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Srikulnath K, Ahmad SF, Singchat W, Panthum T. Why Do Some Vertebrates Have Microchromosomes? Cells 2021; 10:2182. [PMID: 34571831 PMCID: PMC8466491 DOI: 10.3390/cells10092182] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022] Open
Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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22
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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23
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Boman J, Mugal CF, Backström N. The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes. Genome Biol Evol 2021; 13:evab064. [PMID: 33760095 PMCID: PMC8175052 DOI: 10.1093/gbe/evab064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/28/2022] Open
Abstract
Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may-when balanced-promote genetic diversity. Here, we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 resequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.
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Affiliation(s)
- Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Sweden
| | - Carina F Mugal
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Sweden
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24
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de Oliveira JL, Morales AC, Hurst LD, Urrutia AO, Thompson CRL, Wolf JB. Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias. Mol Biol Evol 2021; 38:3247-3266. [PMID: 33871580 PMCID: PMC8321536 DOI: 10.1093/molbev/msab099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection. However, GC-biased gene conversion (gBGC) can also cause deviation from a neutral null. Alternatively, selection has been inferred from CUB in highly expressed genes, but the accuracy of this approach has not been extensively tested, and gBGC can interfere with such extrapolations (e.g., if expression and gene conversion rates covary). It is therefore critical to examine deviations from a mutational null in a species with no gBGC. To achieve this goal, we implement such an analysis in the highly AT rich genome of Dictyostelium discoideum, where we find no evidence of gBGC. We infer neutral CUB under mutational equilibrium to quantify "adaptive codon preference," a nontautologous genome wide quantitative measure of the relative selection strength driving CUB. We observe signatures of purifying selection consistent with selection favoring adaptive codon preference. Preferred codons are not GC rich, underscoring the independence from gBGC. Expression-associated "preference" largely matches adaptive codon preference but does not wholly capture the influence of selection shaping patterns across all genes, suggesting selective constraints associated specifically with high expression. We observe patterns consistent with effects on mRNA translation and stability shaping adaptive codon preference. Thus, our approach to quantifying adaptive codon preference provides a framework for inferring the sources of selection that shape CUB across different contexts within the genome.
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Affiliation(s)
- Janaina Lima de Oliveira
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, 40170-115, Brazil.,Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Atahualpa Castillo Morales
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Laurence D Hurst
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Araxi O Urrutia
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.,Instituto de Ecologia, UNAM, Ciudad de Mexico 04510, Mexico
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Jason B Wolf
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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25
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Yi SV, Goodisman MAD. The impact of epigenetic information on genome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200114. [PMID: 33866804 DOI: 10.1098/rstb.2020.0114] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epigenetic information affects gene function by interacting with chromatin, while not changing the DNA sequence itself. However, it has become apparent that the interactions between epigenetic information and chromatin can, in fact, indirectly lead to DNA mutations and ultimately influence genome evolution. This review evaluates the ways in which epigenetic information affects genome sequence and evolution. We discuss how DNA methylation has strong and pervasive effects on DNA sequence evolution in eukaryotic organisms. We also review how the physical interactions arising from the connections between histone proteins and DNA affect DNA mutation and repair. We then discuss how a variety of epigenetic mechanisms exert substantial effects on genome evolution by suppressing the movement of transposable elements. Finally, we examine how genome expansion through gene duplication is also partially controlled by epigenetic information. Overall, we conclude that epigenetic information has widespread indirect effects on DNA sequences in eukaryotes and represents a potent cause and constraint of genome evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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26
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Card DC, Vonk FJ, Smalbrugge S, Casewell NR, Wüster W, Castoe TA, Schuett GW, Booth W. Genome-wide data implicate terminal fusion automixis in king cobra facultative parthenogenesis. Sci Rep 2021; 11:7271. [PMID: 33790309 PMCID: PMC8012631 DOI: 10.1038/s41598-021-86373-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Facultative parthenogenesis (FP) is widespread in the animal kingdom. In vertebrates it was first described in poultry nearly 70 years ago, and since then reports involving other taxa have increased considerably. In the last two decades, numerous reports of FP have emerged in elasmobranch fishes and squamate reptiles (lizards and snakes), including documentation in wild populations of both clades. When considered in concert with recent evidence of reproductive competence, the accumulating data suggest that the significance of FP in vertebrate evolution has been largely underestimated. Several fundamental questions regarding developmental mechanisms, nonetheless, remain unanswered. Specifically, what is the type of automixis that underlies the production of progeny and how does this impact the genomic diversity of the resulting parthenogens? Here, we addressed these questions through the application of next-generation sequencing to investigate a suspected case of parthenogenesis in a king cobra (Ophiophagus hannah). Our results provide the first evidence of FP in this species, and provide novel evidence that rejects gametic duplication and supports terminal fusion as a mechanism underlying parthenogenesis in snakes. Moreover, we precisely estimated heterozygosity in parthenogenetic offspring and found appreciable retained genetic diversity that suggests that FP in vertebrates has underappreciated evolutionary significance.
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Affiliation(s)
- Daren C Card
- Department of Biology, The University of Texas Arlington, Arlington, TX, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Freek J Vonk
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081HV, Amsterdam, The Netherlands
| | - Sterrin Smalbrugge
- Wildlife Ecology and Conservation Groups, Wageningen University, Wageningen, The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Wolfgang Wüster
- Molecular Ecology and Evolution Group, School of Biological Sciences, Bangor University, Bangor, UK.,Chiricahua Desert Museum, Rodeo, NM, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Arlington, TX, USA
| | - Gordon W Schuett
- Chiricahua Desert Museum, Rodeo, NM, USA.,Department of Biology, Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Warren Booth
- Chiricahua Desert Museum, Rodeo, NM, USA. .,Department of Biological Science, The University of Tulsa, Tulsa, OK, USA.
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27
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Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A 2021; 118:e2016274118. [PMID: 33836575 PMCID: PMC7980453 DOI: 10.1073/pnas.2016274118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Aurélien J Doucet
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Université Côte d'Azur, CNRS, INSERM, Institut de Recherche sur le Cancer et le Vieillissement de Nice, F-06100 Nice, France
| | - Thomas Derrien
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Christophe Hitte
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Laura E Kirby
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Bridget Myers
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Elzbieta Sliwerska
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109;
- Department Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
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28
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Gao NL, He Z, Zhu Q, Jiang P, Hu S, Chen WH. Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:949-957. [PMID: 33741525 PMCID: PMC9403032 DOI: 10.1016/j.gpb.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 05/30/2019] [Accepted: 08/18/2019] [Indexed: 12/04/2022]
Abstract
Coding regions have complex interactions among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes, but the decrease only starts from the ∼ 25th codon. This trend is mostly found in nonsynonymous (ns) sites at which the GC gradient is universal across the eukaryotic genome. Increased GC contents at ns sites result in cheaper amino acids, indicating a universal selection for energy efficiency toward the N-termini of encoded proteins. Within a genome, the decreasing GC gradient is intensified from lowly to highly expressed genes (more and more protein products), further supporting this hypothesis. This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites. Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation. Conversely, the GC gradients at four-fold and two-fold synonymous sites vary across species. They could decrease or increase, suggesting different constraints acting at the GC contents of different codon sites in different species. This study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences, especially efficient energy usage.
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Affiliation(s)
- Na L Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Institute for Computer Science and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Duesseldorf 40225, Germany
| | - Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing 100191, China
| | - Qianhui Zhu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Puzi Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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29
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Berdan EL, Blanckaert A, Butlin RK, Bank C. Deleterious mutation accumulation and the long-term fate of chromosomal inversions. PLoS Genet 2021; 17:e1009411. [PMID: 33661924 PMCID: PMC7963061 DOI: 10.1371/journal.pgen.1009411] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/16/2021] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion.
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Affiliation(s)
- Emma L. Berdan
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | | | - Roger K. Butlin
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Institute of Ecology and Evolution, University of Bern, Switzerland
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30
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Barbhuiya PA, Uddin A, Chakraborty S. Understanding the codon usage patterns of mitochondrial CO genes among Amphibians. Gene 2021; 777:145462. [PMID: 33515725 DOI: 10.1016/j.gene.2021.145462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
A universal phenomenon of using synonymous codons unequally in coding sequences known as codon usage bias (CUB) is observed in all forms of life. Mutation and natural selection drive CUB in many species but the relative role of evolutionary forces varies across species, genes and genomes. We studied the CUB in mitochondrial (mt) CO genes from three orders of Amphibia using bioinformatics approach as no work was reported yet. We observed that CUB of mt CO genes of Amphibians was weak across different orders. Order Caudata had higher CUB followed by Gymnophiona and Anura for all genes and CUB also varied across genes. Nucleotide composition analysis showed that CO genes were AT-rich. The AT content in Caudata was higher than that in Gymnophiona while Anura showed the least content. Multiple investigations namely nucleotide composition, correspondence analysis, parity plot analysis showed that the interplay of mutation pressure and natural selection caused CUB in these genes. Neutrality plot suggested the involvement of natural selection was more than the mutation pressure. The contribution of natural selection was higher in Anura than Gymnophiona and the lowest in Caudata. The codons CGA, TGA, AAA were found to be highly favoured by nature across all genes and orders.
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Affiliation(s)
- Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788150, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788150, Assam, India.
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31
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A Crosstalk on Codon Usage in Genes Associated with Leukemia. Biochem Genet 2020; 59:235-255. [PMID: 32989646 DOI: 10.1007/s10528-020-10000-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) parameter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also prominent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relationship of translational rate was observed with CUB of genes and folding energy.
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32
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Bravo Núñez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE. Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers. eLife 2020; 9:57936. [PMID: 32790622 PMCID: PMC7426094 DOI: 10.7554/elife.57936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Killer meiotic drivers are genetic parasites that destroy ‘sibling’ gametes lacking the driver allele. The fitness costs of drive can lead to selection of unlinked suppressors. This suppression could involve evolutionary tradeoffs that compromise gametogenesis and contribute to infertility. Schizosaccharomyces pombe, an organism containing numerous gamete (spore)-killing wtf drivers, offers a tractable system to test this hypothesis. Here, we demonstrate that in scenarios analogous to outcrossing, wtf drivers generate a fitness landscape in which atypical spores, such as aneuploids and diploids, are advantageous. In this context, wtf drivers can decrease the fitness costs of mutations that disrupt meiotic fidelity and, in some circumstances, can even make such mutations beneficial. Moreover, we find that S. pombe isolates vary greatly in their ability to make haploid spores, with some isolates generating up to 46% aneuploid or diploid spores. This work empirically demonstrates the potential for meiotic drivers to shape the evolution of gametogenesis.
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Affiliation(s)
| | | | - Lauren E Eide
- Stowers Institute for Medical Research, Kansas City, United States.,University of Missouri-Kansas City, Kansas City, United States
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
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33
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Hämälä T, Tiffin P. Biased Gene Conversion Constrains Adaptation in Arabidopsis thaliana. Genetics 2020; 215:831-846. [PMID: 32414868 PMCID: PMC7337087 DOI: 10.1534/genetics.120.303335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/14/2020] [Indexed: 02/01/2023] Open
Abstract
Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better understand constraints on responses to both natural and human-mediated selection. Here, using whole-genome, transcriptome, and methylome data from >600 Arabidopsis thaliana individuals, we set out to identify important features influencing selective constraint. Our analyses reveal that multiple factors underlie the accumulation of maladaptive mutations, including gene expression level, gene network connectivity, and gene-body methylation. We then focus on a feature with major effect, nucleotide composition. The ancestral vs. derived status of segregating alleles suggests that GC-biased gene conversion, a recombination-associated process that increases the frequency of G and C nucleotides regardless of their fitness effects, shapes sequence patterns in A. thaliana Through estimation of mutational effects, we present evidence that biased gene conversion hinders the purging of deleterious mutations and contributes to a genome-wide signal of decreased efficacy of selection. By comparing these results to two outcrossing relatives, Arabidopsis lyrata and Capsella grandiflora, we find that protein evolution in A. thaliana is as strongly affected by biased gene conversion as in the outcrossing species. Last, we perform simulations to show that natural levels of outcrossing in A. thaliana are sufficient to facilitate biased gene conversion despite increased homozygosity due to selfing. Together, our results show that even predominantly selfing taxa are susceptible to biased gene conversion, suggesting that it may constitute an important constraint to adaptation among plant species.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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34
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The Location of the Pseudoautosomal Boundary in Silene latifolia. Genes (Basel) 2020; 11:genes11060610. [PMID: 32486434 PMCID: PMC7348893 DOI: 10.3390/genes11060610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Y-chromosomes contain a non-recombining region (NRY), and in many organisms it was shown that the NRY expanded over time. How and why the NRY expands remains unclear. Young sex chromosomes, where NRY expansion occurred recently or is on-going, offer an opportunity to study the causes of this process. Here, we used the plant Silene latifolia, where sex chromosomes evolved ~11 million years ago, to study the location of the boundary between the NRY and the recombining pseudoautosomal region (PAR). The previous work devoted to the NRY/PAR boundary in S. latifolia was based on a handful of genes with locations approximately known from the genetic map. Here, we report the analysis of 86 pseudoautosomal and sex-linked genes adjacent to the S. latifolia NRY/PAR boundary to establish the location of the boundary more precisely. We take advantage of the dense genetic map and polymorphism data from wild populations to identify 20 partially sex-linked genes located in the “fuzzy boundary”, that rarely recombines in male meiosis. Genes proximal to this fuzzy boundary show no evidence of recombination in males, while the genes distal to this partially-sex-linked region are actively recombining in males. Our results provide a more accurate location for the PAR boundary in S. latifolia, which will help to elucidate the causes of PAR boundary shifts leading to NRY expansion over time.
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35
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Karin BR, Gamble T, Jackman TR. Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements. Mol Biol Evol 2020; 37:904-922. [PMID: 31710677 PMCID: PMC7038749 DOI: 10.1093/molbev/msz263] [Citation(s) in RCA: 20] [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] [Indexed: 12/17/2022] Open
Abstract
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
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Affiliation(s)
- Benjamin R Karin
- Department of Biology, Villanova University, Villanova, PA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA
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36
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Woerner AE, Veeramah KR, Watkins JC, Hammer MF. The Role of Phylogenetically Conserved Elements in Shaping Patterns of Human Genomic Diversity. Mol Biol Evol 2020; 35:2284-2295. [PMID: 30113695 DOI: 10.1093/molbev/msy145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Evolutionary genetic studies have shown a positive correlation between levels of nucleotide diversity and either rates of recombination or genetic distance to genes. Both positive-directional and purifying selection have been offered as the source of these correlations via genetic hitchhiking and background selection, respectively. Phylogenetically conserved elements (CEs) are short (∼100 bp), widely distributed (comprising ∼5% of genome), sequences that are often found far from genes. While the function of many CEs is unknown, CEs also are associated with reduced diversity at linked sites. Using high coverage (>80×) whole genome data from two human populations, the Yoruba and the CEU, we perform fine scale evaluations of diversity, rates of recombination, and linkage to genes. We find that the local rate of recombination has a stronger effect on levels of diversity than linkage to genes, and that these effects of recombination persist even in regions far from genes. Our whole genome modeling demonstrates that, rather than recombination or GC-biased gene conversion, selection on sites within or linked to CEs better explains the observed genomic diversity patterns. A major implication is that very few sites in the human genome are predicted to be free of the effects of selection. These sites, which we refer to as the human "neutralome," comprise only 1.2% of the autosomes and 5.1% of the X chromosome. Demographic analysis of the neutralome reveals larger population sizes and lower rates of growth for ancestral human populations than inferred by previous analyses.
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Affiliation(s)
- August E Woerner
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ.,Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
| | | | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
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37
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Trevino AE, Sinnott-Armstrong N, Andersen J, Yoon SJ, Huber N, Pritchard JK, Chang HY, Greenleaf WJ, Pașca SP. Chromatin accessibility dynamics in a model of human forebrain development. Science 2020; 367:eaay1645. [PMID: 31974223 PMCID: PMC7313757 DOI: 10.1126/science.aay1645] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Abstract
Forebrain development is characterized by highly synchronized cellular processes, which, if perturbed, can cause disease. To chart the regulatory activity underlying these events, we generated a map of accessible chromatin in human three-dimensional forebrain organoids. To capture corticogenesis, we sampled glial and neuronal lineages from dorsal or ventral forebrain organoids over 20 months in vitro. Active chromatin regions identified in human primary brain tissue were observed in organoids at different developmental stages. We used this resource to map genetic risk for disease and to explore evolutionary conservation. Moreover, we integrated chromatin accessibility with transcriptomics to identify putative enhancer-gene linkages and transcription factors that regulate human corticogenesis. Overall, this platform brings insights into gene-regulatory dynamics at previously inaccessible stages of human forebrain development, including signatures of neuropsychiatric disorders.
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Affiliation(s)
- Alexandro E Trevino
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Stanford Human Brain Organogenesis Program, Stanford, CA, USA
| | | | - Jimena Andersen
- Stanford Human Brain Organogenesis Program, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Se-Jin Yoon
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Nina Huber
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
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38
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Castellano D, Eyre-Walker A, Munch K. Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae. Genome Biol Evol 2020; 12:3550-3561. [PMID: 31596481 PMCID: PMC6944223 DOI: 10.1093/gbe/evz215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 12/23/2022] Open
Abstract
DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Denmark
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, Spain
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Denmark
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39
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Subramanian S. Population size influences the type of nucleotide variations in humans. BMC Genet 2019; 20:93. [PMID: 31805852 PMCID: PMC6894472 DOI: 10.1186/s12863-019-0798-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/01/2019] [Indexed: 11/24/2022] Open
Abstract
Background It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Results Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Conclusions Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).
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Affiliation(s)
- Sankar Subramanian
- GeneCology Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia.
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40
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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41
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Hasan AR, Duggal JK, Ness RW. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2019; 224:1339-1348. [PMID: 31222749 DOI: 10.1111/nph.16003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Recombination suppression in sex chromosomes and mating type loci can lead to degeneration as a result of reduced selection efficacy and Muller's ratchet effects. However, genetic exchange in the form of noncrossover gene conversions may still take place within crossover-suppressed regions. Recent work has found evidence that gene conversion may explain the low degrees of allelic differentiation in the dimorphic mating-type locus (MT) of the isogamous alga Chlamydomonas reinhardtii. However, no one has tested whether gene conversion is sufficient to avoid the degeneration of functional sequence within MT. Here, we calculate degree of linkage disequilibrium (LD) across MT as a proxy for recombination rate and investigate its relationship to patterns of population genetic variation and the efficacy of selection in the region. We find that degree of LD predicts selection efficacy across MT, and that purifying selection is stronger in shared genes than in MT-limited genes to the point of being equivalent to that of autosomal genes. We argue that while crossover suppression is needed in the mating-type loci of many isogamous systems, these loci are less likely to experience selection to differentiate further. Thus, recombination can act in these regions and prevent degeneration caused by Hill-Robertson effects.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Jaspreet K Duggal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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42
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Talla V, Soler L, Kawakami T, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species. Genome Biol Evol 2019; 11:2875-2886. [PMID: 31580421 PMCID: PMC6795238 DOI: 10.1093/gbe/evz212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.
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Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Magne Friberg
- Department of Biology, Biodiversity Unit, Lund University, Sweden
| | - Christer Wiklund
- Department of Zoology, Division of Ecology, Stockholm University, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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43
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Sun S, Coelho MA, Heitman J, Nowrousian M. Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet 2019; 15:e1008365. [PMID: 31490920 PMCID: PMC6730849 DOI: 10.1371/journal.pgen.1008365] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In basidiomycetes, the ancestral state is hypothesized to be tetrapolar, with two genetically unlinked MAT loci containing homeodomain transcription factor genes (HD locus) and pheromone and pheromone receptor genes (P/R locus), respectively. Alleles at both loci must differ between mating partners for completion of sexual development. However, there are also basidiomycetes with bipolar mating systems, which can arise through genomic linkage of the HD and P/R loci. In the order Tremellales, bipolarity is found only in the pathogenic Cryptococcus species. Here, we describe the analysis of MAT loci from 24 species of the Trichosporonales, a sister order to the Tremellales. In all of the species analyzed, the MAT loci are fused and a single HD gene is present in each mating type, similar to the organization in the pathogenic Cryptococci. However, the HD and P/R allele combinations in the Trichosporonales are different from those in the pathogenic Cryptococci. This and the existence of tetrapolar species in the Tremellales suggest that fusion of the HD and P/R loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions, similar to previous findings in other fungal groups. Unlike the fused MAT loci in several other basidiomycete lineages though, the gene content and gene order within the fused MAT loci are highly conserved in the Trichosporonales, and there is no apparent suppression of recombination extending from the MAT loci to adjacent chromosomal regions, suggesting different mechanisms for the evolution of physically linked MAT loci in these groups.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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Borges R, Szöllősi GJ, Kosiol C. Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models. Genetics 2019; 212:1321-1336. [PMID: 31147380 PMCID: PMC6707462 DOI: 10.1534/genetics.119.302074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/20/2019] [Indexed: 11/18/2022] Open
Abstract
As multi-individual population-scale data become available, more complex modeling strategies are needed to quantify genome-wide patterns of nucleotide usage and associated mechanisms of evolution. Recently, the multivariate neutral Moran model was proposed. However, it was shown insufficient to explain the distribution of alleles in great apes. Here, we propose a new model that includes allelic selection. Our theoretical results constitute the basis of a new Bayesian framework to estimate mutation rates and selection coefficients from population data. We apply the new framework to a great ape dataset, where we found patterns of allelic selection that match those of genome-wide GC-biased gene conversion (gBGC). In particular, we show that great apes have patterns of allelic selection that vary in intensity-a feature that we correlated with great apes' distinct demographies. We also demonstrate that the AT/GC toggling effect decreases the probability of a substitution, promoting more polymorphisms in the base composition of great ape genomes. We further assess the impact of GC-bias in molecular analysis, and find that mutation rates and genetic distances are estimated under bias when gBGC is not properly accounted for. Our results contribute to the discussion on the tempo and mode of gBGC evolution, while stressing the need for gBGC-aware models in population genetics and phylogenetics.
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Affiliation(s)
- Rui Borges
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Wien, Austria
| | - Gergely J Szöllősi
- Department of Biological Physics, MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Eötvös University, Pázmány P. stny. 1A, Budapest 1117, Hungary
| | - Carolin Kosiol
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Wien, Austria
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife KY16 9TH, UK
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45
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A century of bias in genetics and evolution. Heredity (Edinb) 2019; 123:33-43. [PMID: 31189901 DOI: 10.1038/s41437-019-0194-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 02/08/2023] Open
Abstract
Mendel proposed that the heritable material is particulate and that transmission of alleles is unbiased. An assumption of unbiased transmission was necessary to show how variation can be preserved in the absence of selection, so overturning an early objection to Darwinism. In the second half of the twentieth century, it was widely recognised that even strongly deleterious alleles can invade if they have strongly biased transmission (i.e. strong segregation distortion). The spread of alleles with distorted segregation can explain many curiosities. More recently, the selectionist-neutralist duopoly was broken by the realisation that biased gene conversion can explain phenomena such as mammalian isochore structures. An initial focus on unbiased transmission in 1919, has thus given way to an interest in biased transmission in 2019. A focus on very weak bias is now possible owing to technological advances, although technical biases may put a limit on resolving power. To understand the relevance of weak bias we could profit from having the concept of the effectively Mendelian allele, a companion to the effectively neutral allele. Understanding the implications of unbiased and biased transmission may, I suggest, be a good way to teach evolution so as to avoid psychological biases.
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Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol Biol Evol 2019; 35:1668-1677. [PMID: 29659991 PMCID: PMC5995167 DOI: 10.1093/molbev/msy058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for nonrecombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects, and their sexual sister-species. We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
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Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten M Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emeric Figuet
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Nicolas Galtier
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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47
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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48
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Palmer M, Venter SN, Coetzee MP, Steenkamp ET. Prokaryotic species are sui generis evolutionary units. Syst Appl Microbiol 2019; 42:145-158. [DOI: 10.1016/j.syapm.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/25/2022]
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49
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Weng Z, Wolc A, Su H, Fernando RL, Dekkers JCM, Arango J, Settar P, Fulton JE, O'Sullivan NP, Garrick DJ. Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens. J Anim Sci Biotechnol 2019; 10:20. [PMID: 30891237 PMCID: PMC6390344 DOI: 10.1186/s40104-019-0332-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/31/2019] [Indexed: 12/15/2022] Open
Abstract
Background The frequency of recombination events varies across the genome and between individuals, which may be related to some genomic features. The objective of this study was to assess the frequency of recombination events and to identify QTL (quantitative trait loci) for recombination rate in two purebred layer chicken lines. Methods A total of 1200 white-egg layers (WL) were genotyped with 580 K SNPs and 5108 brown-egg layers (BL) were genotyped with 42 K SNPs (single nucleotide polymorphisms). Recombination events were identified within half-sib families and both the number of recombination events and the recombination rate was calculated within each 0.5 Mb window of the genome. The 10% of windows with the highest recombination rate on each chromosome were considered to be recombination hotspots. A BayesB model was used separately for each line to identify genomic regions associated with the genome-wide number of recombination event per meiosis. Regions that explained more than 0.8% of genetic variance of recombination rate were considered to harbor QTL. Results Heritability of recombination rate was estimated at 0.17 in WL and 0.16 in BL. On average, 11.3 and 23.2 recombination events were detected per individual across the genome in 1301 and 9292 meioses in the WL and BL, respectively. The estimated recombination rates differed significantly between the lines, which could be due to differences in inbreeding levels, and haplotype structures. Dams had about 5% to 20% higher recombination rates per meiosis than sires in both lines. Recombination rate per 0.5 Mb window had a strong negative correlation with chromosome size and a strong positive correlation with GC content and with CpG island density across the genome in both lines. Different QTL for recombination rate were identified in the two lines. There were 190 and 199 non-overlapping recombination hotspots detected in WL and BL respectively, 28 of which were common to both lines. Conclusions Differences in the recombination rates, hotspot locations, and QTL regions associated with genome-wide recombination were observed between lines, indicating the breed-specific feature of detected recombination events and the control of recombination events is a complex polygenic trait. Electronic supplementary material The online version of this article (10.1186/s40104-019-0332-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ziqing Weng
- 1Department of Animal Science, Iowa State University, Ames, IA 50010 USA
| | - Anna Wolc
- 1Department of Animal Science, Iowa State University, Ames, IA 50010 USA.,2Hy-Line International, Dallas Center, IA 50063 USA
| | - Hailin Su
- 1Department of Animal Science, Iowa State University, Ames, IA 50010 USA
| | - Rohan L Fernando
- 1Department of Animal Science, Iowa State University, Ames, IA 50010 USA
| | - Jack C M Dekkers
- 1Department of Animal Science, Iowa State University, Ames, IA 50010 USA
| | - Jesus Arango
- 2Hy-Line International, Dallas Center, IA 50063 USA
| | - Petek Settar
- 2Hy-Line International, Dallas Center, IA 50063 USA
| | | | | | - Dorian J Garrick
- 1Department of Animal Science, Iowa State University, Ames, IA 50010 USA.,3AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North, 4442 New Zealand
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50
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Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
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