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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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2
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Liu K, Xie N, Wang Y, Liu X. The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:907-917. [PMID: 37661218 DOI: 10.1007/s10126-023-10248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Long-read sequencing technologies can generate highly contiguous genome assemblies compared to short-read methods. However, their higher cost often poses a significant barrier. To address this, we explore the utilization of mapping-based genome assembly and reference-guided assembly as cost-effective alternative approaches. We assess the efficacy of these approaches in improving the contiguity of Clarias batrachus and Culter alburnus draft genomes. Our findings demonstrate that employing an iterative mapping strategy leads to a reduction in assembly errors. Specifically, after three iterations, the Mismatches per 100 kbp value for the C. batrachus genome decreased from 2447.20 to 2432.67, reaching a minimum of 2422.67 after two iterations. Additionally, the N50 value for the C. batrachus genome increased from 362,143 to 1,315,126 bp, with a maximum of 1,315,403 bp after two iterations. Furthermore, we achieved Mismatches per 100 kbp values of 3.70 for the reference-guided assembly of C. batrachus and 0.34 for C. alburnus. Correspondingly, the N50 value for the C. batrachus and C. alburnus genomes increased from 362,143 bp and 3,686,385 bp to 2,026,888 bp and 43,735,735 bp, respectively. Finally, we successfully utilized the improved C. batrachus and C. alburnus genomes to compare genome studies using the combined approach of Ragout and Ragtag. Through a comprehensive comparative analysis of mapping-based and reference-guided genome assembly methods, we shed light on the specific contributions of reference-guided assembly in reducing assembly errors and improving assembly continuity and integrity. These advancements establish reference-guided assembly and the utilization of in silico libraries as a promising and suitable approach for comparative genomics studies.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Yuxi Wang
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Xinyi Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
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3
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Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions. Genetica 2023:10.1007/s10709-023-00185-x. [PMID: 36940055 DOI: 10.1007/s10709-023-00185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/14/2023] [Indexed: 03/21/2023]
Abstract
Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.
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4
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Reducing Complications and Enhancing the Functional Outcome of Total Hip Arthroplasty without Increasing Operation Time by Repairing Posterolateral Soft Tissues. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:8364423. [PMID: 36176926 PMCID: PMC9499770 DOI: 10.1155/2022/8364423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022]
Abstract
Total hip arthroplasty (THA) surgeries are increasing annually. Despite continuous improvements in the surgical technique and prosthetic design, there is still no consensus on whether it is beneficial to reconstruct the posterolateral soft tissue. This paper systematically reviews randomized controlled trials (RCTs) addressing the efficacy and safety of posterolateral soft tissue during total hip replacement to provide evidence-based guidance for clinical practice. We searched PubMed, EMBASE, Cochrane Library, CNKI, and Wanfang databases for RCTs. Experimental results show that repair of the posterolateral soft tissue can reduce complications and improve the function of total hip arthroplasty without increasing operative time.
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5
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Bemmels JB, Haddrath O, Colbourne RM, Robertson HA, Weir JT. Legacy of supervolcanic eruptions on population genetic structure of brown kiwi. Curr Biol 2022; 32:3389-3397.e8. [PMID: 35728597 DOI: 10.1016/j.cub.2022.05.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
Supervolcanoes are volcanoes capable of mega-colossal eruptions that emit more than 1,000 km3 of ash and other particles.1 The earth's most recent mega-colossal eruption was the Oruanui eruption of the Taupo supervolcano 25,580 years before present (YBP) on the central North Island of New Zealand.2 This eruption blanketed major swaths of the North Island in thick layers of ash and igneous rock,2,3 devastating habitats and likely causing widespread population extinctions.4-7 An additional devastating super-colossal eruption (>100 km3) of the Taupo supervolcano occurred approximately 1,690 YBP.8 The impacts of such massive but ephemeral natural disasters on contemporary population genetic structure remain underexplored. Here, we combined data for 4,951 SNPs with spatially explicit demographic and coalescent models within an approximate Bayesian computation framework to test the drivers of genetic structure in brown kiwi (Apteryx mantelli). Our results strongly support the importance of eruptions of the Taupo supervolcano in restructuring pre-existing geographic patterns of population differentiation and genetic diversity. Range shifts due to climatic oscillations-a frequent explanation for genetic structure9-are insufficient to fully explain the empirical data. Meanwhile, recent range contraction and fragmentation due to historically documented anthropogenic habitat alteration adds no explanatory power to our models. Our results support a major role for cycles of destruction and post-volcanic recolonization in restructuring the population genomic landscape of brown kiwi and highlight how ancient and ephemeral mega-disasters may leave a lasting legacy on patterns of intraspecific genetic variation.
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Affiliation(s)
- Jordan B Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Oliver Haddrath
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Rogan M Colbourne
- Department of Conservation, PO Box 10420, Wellington 6140, New Zealand
| | - Hugh A Robertson
- Department of Conservation, PO Box 10420, Wellington 6140, New Zealand
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada.
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6
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Okuno M, Mizushima S, Kuroiwa A, Itoh T. Analysis of Sex Chromosome Evolution in the Clade Palaeognathae from Phased Genome Assembly. Genome Biol Evol 2021; 13:6413640. [PMID: 34718546 PMCID: PMC8599748 DOI: 10.1093/gbe/evab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Birds in the clade Palaeognathae, excluding Tinamiformes, have morphologically conserved karyotypes and less differentiated ZW sex chromosomes compared with those of other birds. In particular, the sex chromosomes of the ostrich and emu have exceptionally large recombining pseudoautosomal regions (PARs), whereas non-PARs are classified into two strata according to the date of their origins: stratum 0 and stratum 1 (S1). However, the construction and analysis of the genome sequences in these regions in the clade Palaeognathae can be challenging because assembling the S1 region is difficult owing to low sequence diversity between gametologs (Z-linked and W-linked sequences). We addressed this issue by applying the Platanus-allee assembler and successfully constructed the haplotype-resolved (phased) assembly for female emu, cassowary, and ostrich using only sequence read data derived from the Illumina platform. Comparative genomic and phylogenetic analyses based on assembled Z-linked and W-linked sequences confirmed that the S1 region of emu and cassowary formed in their common ancestor. Moreover, the interspersed repetitive sequence landscapes in the S1 regions of female emu showed an expansion of younger repetitive elements in the W-linked S1 region, suggesting an interruption in homologous recombination in the S1 region. These results provide novel insights into the trajectory of sex chromosome evolution in the clade Palaeognathae and suggest that the Illumina-based phased assembly method is an effective approach for elucidating the evolutionary process underlying the transition from homomorphic to differentiated sex chromosomes.
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Affiliation(s)
- Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Shusei Mizushima
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Asato Kuroiwa
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
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7
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Wang Z, Zhang J, Xu X, Witt C, Deng Y, Chen G, Meng G, Feng S, Xu L, Szekely T, Zhang G, Zhou Q. Phylogeny and sex chromosome evolution of palaeognathae. J Genet Genomics 2021; 49:109-119. [PMID: 34872841 DOI: 10.1016/j.jgg.2021.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/30/2022]
Abstract
Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of "evolutionary strata". Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate the "defeminization" of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females that evolved in their common ancestors.
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Affiliation(s)
- Zongji Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria; Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Jilin Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Xiaoman Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Christopher Witt
- Department of Biology and the Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Yuan Deng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Guanliang Meng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
| | - Tamas Szekely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Milner Center for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA1 7AY, UK
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria; Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China.
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Liu J, Wang Z, Li J, Xu L, Liu J, Feng S, Guo C, Chen S, Ren Z, Rao J, Wei K, Chen Y, Jarvis ED, Zhang G, Zhou Q. A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Res 2021; 31:497-511. [PMID: 33408157 PMCID: PMC7919449 DOI: 10.1101/gr.271569.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023]
Abstract
Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level genome assemblies of 11 other bird and one turtle species. We found ratites exhibited the lowest numbers of intra- and inter-chromosomal changes among birds since their divergence with turtles. The small-sized and gene-rich emu microchromosomes have frequent inter-chromosomal contacts that are associated with housekeeping genes, which appears to be driven by clustering their centromeres in the nuclear interior, away from the macrochromosomes in the nuclear periphery. Unlike nonratite birds, only less than one-third of the emu W Chromosome regions have lost homologous recombination and diverged between the sexes. The emu W is demarcated into a highly heterochromatic region (WS0) and another recently evolved region (WS1) with only moderate sequence divergence with the Z Chromosome. WS1 has expanded its inactive chromatin compartment, increased chromatin contacts within the region, and decreased contacts with the nearby regions, possibly influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
| | - Zongji Wang
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
- Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo 315100, China
| | - Jing Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
| | - Jiaqi Liu
- Wuhan Gooalgene Technology Company, Wuhan 430070, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Chunxue Guo
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Shengchan Chen
- Longteng Ecological Culture Company, Limited, Zhashui 711400, China
| | - Zhanjun Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jinpeng Rao
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Kai Wei
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Yuezhou Chen
- Jianzhou Poultry Industry Company, Limited, Yong'an 366000, China
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, New York 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
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9
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Tian S, Zhou X, Phuntsok T, Zhao N, Zhang D, Ning C, Li D, Zhao H. Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens. iScience 2020; 23:101644. [PMID: 33103083 PMCID: PMC7578744 DOI: 10.1016/j.isci.2020.101644] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/19/2020] [Accepted: 09/30/2020] [Indexed: 12/05/2022] Open
Abstract
The genetic footprints of adaptations to naturally occurring tropical stress along with domestication are poorly reported in chickens. Here, by conducting population genomic analyses of 67 chickens inhabiting distinct climates, we found signals of gene flow from Tibetan chickens to Sri Lankan and Saudi Arabian breeds and identified 12 positively selected genes that are likely involved in genetic adaptations to both tropical desert and tropical monsoon island climates. Notably, in tropical desert climate, advantageous alleles of TLR7 and ZC3HAV1, which could inhibit replication of viruses in cells, suggest immune adaptation to the defense against zoonotic diseases in chickens. Furthermore, comparative genomic analysis showed that four genes (OC90, PLA2G12B, GPR17 and TNFRSF11A) involved in arachidonic acid metabolism have undergone convergent adaptation to tropical desert climate between birds and mammals. Our study offers insights into the genetic mechanisms of adaptations to tropical climates in birds and other animals and provides practical value for breeding design and medical research on avian viruses.
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Affiliation(s)
- Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Tashi Phuntsok
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Ning Zhao
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Dejing Zhang
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Chunyou Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
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10
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Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
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Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
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11
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Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome Biol Evol 2020; 11:2376-2390. [PMID: 31329234 PMCID: PMC6735826 DOI: 10.1093/gbe/evz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.
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Affiliation(s)
- Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Timothy B Sackton
- Informatics Group, Division of Science, Harvard University
- Corresponding author: E-mail:
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12
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Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up.
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13
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O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 2018; 19:171. [PMID: 30355328 PMCID: PMC6201548 DOI: 10.1186/s13059-018-1550-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/24/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. RESULTS We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. CONCLUSIONS The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.
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Affiliation(s)
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Lucas Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Sophie Bennett
- School of Biosciences, University of Kent, Canterbury, UK
| | - Eden A Slack
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Emily Allanson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
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14
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Piégu B, Arensburger P, Guillou F, Bigot Y. But where did the centromeres go in the chicken genome models? Chromosome Res 2018; 26:297-306. [PMID: 30225548 DOI: 10.1007/s10577-018-9585-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022]
Abstract
The chicken genome was the third vertebrate to be sequenced. To date, its sequence and feature annotations are used as the reference for avian models in genome sequencing projects developed on birds and other Sauropsida species, and in genetic studies of domesticated birds of economic and evolutionary biology interest. Therefore, an accurate description of this genome model is important to a wide number of scientists. Here, we review the location and features of a very basic element, the centromeres of chromosomes in the galGal5 genome model. Centromeres are elements that are not determined by their DNA sequence but by their epigenetic status, in particular by the accumulation of the histone-like protein CENP-A. Comparison of data from several public sources (primarily marker probes flanking centromeres using fluorescent in situ hybridization done on giant lampbrush chromosomes and CENP-A ChIP-seq datasets) with galGal5 annotations revealed that centromeres are likely inappropriately mapped in 9 of the 16 galGal5 chromosome models in which they are described. Analysis of karyology data confirmed that the location of the main CENP-A peaks in chromosomes is the best means of locating the centromeres in 25 galGal5 chromosome models, the majority of which (16) are fully sequenced and assembled. This data re-analysis reaffirms that several sources of information should be examined to produce accurate genome annotations, particularly for basic structures such as centromeres that are epigenetically determined.
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Affiliation(s)
- Benoît Piégu
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA, 91768, USA
| | - Florian Guillou
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Yves Bigot
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France.
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15
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Yazdi HP, Ellegren H. A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution. Genome Biol Evol 2018; 10:2049-2060. [PMID: 30099482 PMCID: PMC6105114 DOI: 10.1093/gbe/evy163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (≈60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.
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Affiliation(s)
- Homa Papoli Yazdi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
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16
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You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo MC, Wang X, Deyholos MK, Cloutier S. Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:371-384. [PMID: 29681136 DOI: 10.1111/tpj.13944] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 05/19/2023]
Abstract
Genomes of varying sizes have been sequenced with next-generation sequencing platforms. However, most reference sequences include draft unordered scaffolds containing chimeras caused by mis-scaffolding. A BioNano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (Linum usitatissimum L., 2n = 30, about 373 Mb), which consisted of 3852 scaffolds larger than 1 kb and totalling 300.6 Mb. The high-resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG contigs with an N50 of 2.15 Mb. A total of 622 scaffolds (286.6 Mb, 94.9%) aligned to 211 BNG contigs (298.6 Mb, 94.2%). Of those, 99 scaffolds, diagnosed to contain assembly errors, were refined into 225 new scaffolds. Using the newly refined scaffold sequences and the validated bacterial artificial chromosome-based physical map of CDC Bethune, the 211 BNG contigs were scaffolded into 94 super-BNG contigs (N50 of 6.64 Mb) that were further assigned to the 15 flax chromosomes using the genetic map. The pseudomolecules total about 316 Mb, with individual chromosomes of 15.6 to 29.4 Mb, and cover 97% of the annotated genes. Evidence from the chromosome-scale pseudomolecules suggests that flax has undergone palaeopolyploidization and mesopolyploidization events, followed by rearrangements and deletions or fusion of chromosome arms from an ancient progenitor with a haploid chromosome number of eight.
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Affiliation(s)
- Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
- State Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Gaofeng Jia
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Liqiang He
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | | | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
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17
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Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 2017; 49:387-394. [PMID: 28135246 PMCID: PMC5359078 DOI: 10.1038/ng.3778] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/29/2016] [Indexed: 12/14/2022]
Abstract
After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males ZZ, but in mammals females are XX and males XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly-expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction related genes on sex chromosomes may be specific to the male germ line.
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18
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Kapusta A, Suh A. Evolution of bird genomes-a transposon's-eye view. Ann N Y Acad Sci 2016; 1389:164-185. [DOI: 10.1111/nyas.13295] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics; University of Utah School of Medicine; Salt Lake City Utah
| | - Alexander Suh
- Department of Evolutionary Biology (EBC); Uppsala University; Uppsala Sweden
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19
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Jarvis ED. Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. Annu Rev Anim Biosci 2016; 4:45-59. [PMID: 26884102 DOI: 10.1146/annurev-animal-021815-111216] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate the large-scale Avian Phylogenomics Project, which collected and sequenced genomes of 48 bird species representing most currently classified orders to address a range of questions in phylogenomics and comparative genomics. The consortium was able to answer questions not previously possible with just a few genomes. This success spurred on the creation of a project to sequence the genomes of at least one individual of all extant ∼10,500 bird species. The initiation of this project has led us to consider what questions now impossible to answer could be answered with all genomes, and could drive new questions now unimaginable. These include the generation of a highly resolved family tree of extant species, genome-wide association studies across species to identify genetic substrates of many complex traits, redefinition of species and the species concept, reconstruction of the genomes of common ancestors, and generation of new computational tools to address these questions. Here I present visions for the future by posing and answering questions regarding what scientists could potentially do with available genomes of an entire vertebrate class.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina 27710
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20
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Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Rakownikow Jersie-Christensen R, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee RDE, Kwekason A, Ecker M, Kolska Horwitz L, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K, Collins MJ. Protein sequences bound to mineral surfaces persist into deep time. eLife 2016; 5. [PMID: 27668515 PMCID: PMC5039028 DOI: 10.7554/elife.17092] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI:http://dx.doi.org/10.7554/eLife.17092.001 The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved. Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences. In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Demarchi et al. have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences. Using a computer simulation method called molecular dynamics, Demarchi et al. calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi et al. recommend using as a standard for ancient protein studies. Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms. DOI:http://dx.doi.org/10.7554/eLife.17092.002
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Shaun Hall
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | - Colin L Freeman
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jos Woolley
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Molly K Crisp
- Department of Chemistry, University of York, York, United Kingdom
| | - Julie Wilson
- Department of Chemistry, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom
| | - Anna Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jessica Thomas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Curtis W Marean
- Institute of Human Origins, SHESC, Arizona State University, Tempe, United States.,Centre for Coastal Palaeoscience, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Peter Ditchfield
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jacqueline F Hamilton
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Martyn W Ward
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Chunting Michelle Wang
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Marvin D Shaw
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, United States
| | | | - Ross DE MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, United States
| | | | - Michaela Ecker
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Michael Chazan
- Department of Anthropology, University of Toronto, Toronto, Canada.,Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein, South Africa
| | - Roland Kröger
- Department of Physics, University of York, York, United Kingdom
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, York, United Kingdom.,Centre of Excellence in Mass Spectrometry, University of York, New York, United States
| | - John H Harding
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kirsty Penkman
- Department of Chemistry, University of York, York, United Kingdom
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
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21
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Staňková H, Hastie AR, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Doležel J, Šimková H. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1523-31. [PMID: 26801360 PMCID: PMC5066648 DOI: 10.1111/pbi.12513] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 05/09/2023]
Abstract
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
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Affiliation(s)
- Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Saki Chan
- BioNano Genomics, San Diego, CA, USA
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Paul Visendi
- Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
| | - Satomi Hayashi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Mammalian X homolog acts as sex chromosome in lacertid lizards. Heredity (Edinb) 2016; 117:8-13. [PMID: 26980341 DOI: 10.1038/hdy.2016.18] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/16/2015] [Accepted: 02/02/2016] [Indexed: 01/13/2023] Open
Abstract
Among amniotes, squamate reptiles are especially variable in their mechanisms of sex determination; however, based largely on cytogenetic data, some lineages possess highly evolutionary stable sex chromosomes. The still very limited knowledge of the genetic content of squamate sex chromosomes precludes a reliable reconstruction of the evolutionary history of sex determination in this group and consequently in all amniotes. Female heterogamety with a degenerated W chromosome typifies the lizards of the family Lacertidae, the widely distributed Old World clade including several hundreds of species. From the liver transcriptome of the lacertid Takydromus sexlineatus female, we selected candidates for Z-specific genes as the loci lacking single-nucleotide polymorphisms. We validated the candidate genes through the comparison of the copy numbers in the female and male genomes of T. sexlineatus and another lacertid species, Lacerta agilis, by quantitative PCR that also proved to be a reliable technique for the molecular sexing of the studied species. We suggest that this novel approach is effective for the detection of Z-specific and X-specific genes in lineages with degenerated W, respectively Y chromosomes. The analyzed gene content of the Z chromosome revealed that lacertid sex chromosomes are not homologous with those of other reptiles including birds, but instead the genes have orthologs in the X-conserved region shared by viviparous mammals. It is possible that this part of the vertebrate genome was independently co-opted for the function of sex chromosomes in viviparous mammals and lacertids because of its content of genes involved in gonad differentiation.
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