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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: 0] [Impact Index Per Article: 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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Griffin DK, Larkin DM, O’Connor RE, Romanov MN. Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants. Animals (Basel) 2022; 13:ani13010106. [PMID: 36611715 PMCID: PMC9817885 DOI: 10.3390/ani13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species. The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine-Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
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Affiliation(s)
- Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence:
| | - Denis M. Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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Zhu F, Yin ZT, Wang Z, Smith J, Zhang F, Martin F, Ogeh D, Hincke M, Lin FB, Burt DW, Zhou ZK, Hou SS, Zhao QS, Li XQ, Ding SR, Li GS, Yang FX, Hao JP, Zhang Z, Lu LZ, Yang N, Hou ZC. Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat Commun 2021; 12:5932. [PMID: 34635656 PMCID: PMC8505442 DOI: 10.1038/s41467-021-26272-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/21/2021] [Indexed: 01/23/2023] Open
Abstract
Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed "missing genes" in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Zheng Wang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Fan Zhang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maxwell Hincke
- Department of Cellular and Molecular Medicine, Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, KIH 8M5, Canada
| | - Fang-Bing Lin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - David W Burt
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zheng-Kui Zhou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Shui-Sheng Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Qiang-Sen Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiao-Qin Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Si-Ran Ding
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Guan-Sheng Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Fang-Xi Yang
- Beijing Golden-Star Inc., Beijing, 100076, China
| | - Jing-Pin Hao
- Beijing Golden-Star Inc., Beijing, 100076, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Li-Zhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021; 10:cells10020362. [PMID: 33572408 PMCID: PMC7916199 DOI: 10.3390/cells10020362] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
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Li J, Zhang J, Liu J, Zhou Y, Cai C, Xu L, Dai X, Feng S, Guo C, Rao J, Wei K, Jarvis ED, Jiang Y, Zhou Z, Zhang G, Zhou Q. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. Gigascience 2021; 10:giaa142. [PMID: 33406261 PMCID: PMC7787181 DOI: 10.1093/gigascience/giaa142] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/31/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. RESULTS A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. CONCLUSIONS Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.
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Affiliation(s)
- Jing Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jilin Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 5 Nobels väg, Stockholm 17177, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, 1 Universitätsring, Vienna 1090, Austria
| | - Yang Zhou
- BGI-Shenzhen, 146 Beishan Industrial Zone, Shenzhen 518083, China
| | - Cheng Cai
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Luohao Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, 1 Universitätsring, Vienna 1090, Austria
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 3 Taicheng Road, Yangling 712100, China
| | - Shaohong Feng
- BGI-Shenzhen, 146 Beishan Industrial Zone, Shenzhen 518083, China
| | - Chunxue Guo
- BGI-Shenzhen, 146 Beishan Industrial Zone, Shenzhen 518083, China
| | - Jinpeng Rao
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310052, China
| | - Kai Wei
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310052, China
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Ave, NY 10065, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 3 Taicheng Road, Yangling 712100, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, 12 Zhong Guan Cun Da Jie, Beijing, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 10 Nørregade, DK-2100 Copenhagen, Denmark
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 East Jiaochang Road, 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, 866 Yuhangtang Road, Hangzhou 310058, China
- Department of Neuroscience and Developmental Biology, University of Vienna, 1 Universitätsring, Vienna 1090, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310052, China
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Whole genome re-sequencing of crested traits and expression analysis of key candidate genes in duck. Gene 2019; 729:144282. [PMID: 31838250 DOI: 10.1016/j.gene.2019.144282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 02/01/2023]
Abstract
The crested duck was a duck breed which features a topknot of feathers on the back of their head. In order to explain the reason of crest, we anatomy the head of some crested ducks. The anatomical structures showed that there was a fat body in the head and a hole in the skull. To determine the reason for the formation of the crest, we used whole genome re-sequencing to detect SNPs and InDels in three crested duck and three normal crested duck (without crest). There were 785,202 unique SNPs and 105,596 unique InDels include in crested duck. There were 14,591 SNPs containing genes and 13,784 InDels continuing genes were mapped on BGI_duck_1.0 by BWA 0.7.16a software. We use KEGG and GO to classification the SNP and InDel containing genes function. The PPI network of SNP containing genes and InDels containing genes was constructed by STRING. The result of PPI and KEGG analysis shown that the formation of crest might include feather development, fatty acid deposition, and skull hypoplasia. To determine the regulated of SNP containing genes and InDels containing genes, which related the different trait, of miRNA we used mirmap to predicted target miRNA of those genes. The miRNA-genes network constructed by Cytoscape. In conclusion, the formation of the crest was a complex process. The fatty acid metabolism block, feather growth and skull hypoplasia might lead crest formation. The tissue expression of four candidate genes showed that they were closely related to the formation of the trait, and could be used as important candidate genes to further elaborate the molecular mechanism of their function.
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Zhu F, Cheng SR, Yang YZ, Hao JP, Yang FX, Hou ZC. Genome-Wide Association Study of Growth and Feeding Traits in Pekin Ducks. Front Genet 2019; 10:702. [PMID: 31404312 PMCID: PMC6676418 DOI: 10.3389/fgene.2019.00702] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 07/03/2019] [Indexed: 12/16/2022] Open
Abstract
Growth rate and feeding efficiency are the most important economic traits for meat animals. Pekin duck is one of the major global breeds of meat-type duck. This study aims to identify QTL for duck growth and feeding efficiency traits in order to assist artificial selection. In this study, the growth and feeding related phenotypes of 639 Pekin ducks were recorded, and each individual genotype was evaluated using a genotyping-by-sequencing (GBS) protocol. The genetic parameters for growth and feeding efficiency related traits were estimated. Genome-wide association analysis (GWAS) was then performed for these traits. In total, 15 non-overlapping QTLs for the measured traits and 12 significant SNPs for feed efficiency traits were discovered using a mixed linear model. The most significant loci of feed intake (FI) is located in a 182Mb region on Chr1, which is downstream of gene RNF17, and can explain 2.3% of the phenotypic variation. This locus is also significantly associated with residual feed intake (RFI), and can explain 3% of this phenotypic variation. Among 12 SNPs associated with the feed conversion ratio (FCR), the most significant SNP (P-value = 1.65E-06), which was located in the region between the 3rd and 4th exon of the SORCS1 gene on Chr6, explained 3% of the phenotypic variance. Using gene-set analysis, a total of two significant genes were detected be associated with RFI on Chr1. This study is the first GWAS for growth and feeding efficiency related traits in ducks. Our results provide a list of candidate genes for marker assisted selection for growth and feeding efficiency, and also help to better understand the genetic mechanisms of feed efficiency and growth in ducks.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Si-Rui Cheng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Yu-Ze Yang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Jin-Ping Hao
- Duck Industry Center, Beijing Golden Star Duck Inc., Beijing, China
| | - Fang-Xi Yang
- Duck Industry Center, Beijing Golden Star Duck Inc., Beijing, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
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Griffin DK, Larkin DM, O'Connor RE. Time lapse: A glimpse into prehistoric genomics. Eur J Med Genet 2019; 63:103640. [PMID: 30922926 PMCID: PMC7026692 DOI: 10.1016/j.ejmg.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/10/2019] [Indexed: 11/28/2022]
Abstract
For the purpose of this review, ‘time-lapse’ refers to the reconstruction of ancestral (in this case dinosaur) karyotypes using genome assemblies of extant species. Such reconstructions are only usually possible when genomes are assembled to ‘chromosome level’ i.e. a complete representation of all the sequences, correctly ordered contiguously on each of the chromosomes. Recent paleontological evidence is very clear that birds are living dinosaurs, the latest example of dinosaurs emerging from a catastrophic extinction event. Non-avian dinosaurs (ever present in the public imagination through art, and broadcast media) emerged some 240 million years ago and have displayed incredible phenotypic diversity. Here we report on our recent studies to infer the overall karyotype of the Theropod dinosaur lineage from extant avian chromosome level genome assemblies. Our work first focused on determining the likely karyotype of the avian ancestor (most likely a chicken-sized, two-legged, feathered, land dinosaur from the Jurassic period) finding karyotypic similarity to the chicken. We then took the work further to determine the likely karyotype of the bird-lizard ancestor and the chromosomal changes (chiefly translocations and inversions) that occurred between then and modern birds. A combination of bioinformatics and cross-species fluorescence in situ hybridization (zoo-FISH) uncovered a considerable number of translocations and fissions from a ‘lizard-like’ genome structure of 2n = 36–46 to one similar to that of soft-shelled turtles (2n = 66) from 275 to 255 million years ago (mya). Remarkable karyotypic similarities between some soft-shelled turtles and chicken suggests that there were few translocations from the bird-turtle ancestor (plus ∼7 fissions) through the dawn of the dinosaurs and pterosaurs, through the theropod linage and on to most to modern birds. In other words, an avian-like karyotype was in place about 240mya when the dinosaurs and pterosaurs first emerged. We mapped 49 chromosome inversions from then to the present day, uncovering some gene ontology enrichment in evolutionary breakpoint regions. This avian-like karyotype with its many (micro)chromosomes provides the basis for variation (the driver of natural selection) through increased random segregation and recombination. It may therefore contribute to the ability of dinosaurs to survive multiple extinction events, emerging each time as speciose and diverse.
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Affiliation(s)
- Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK.
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. R.O'
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Deng MT, Zhu F, Yang YZ, Yang FX, Hao JP, Chen SR, Hou ZC. Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks. BMC Genomics 2019; 20:1. [PMID: 30606130 PMCID: PMC6318962 DOI: 10.1186/s12864-018-5379-1] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/16/2018] [Indexed: 12/26/2022] Open
Abstract
Background Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. Results We measured 18 carcass traits in 639 Pekin ducks and performed genotyping using genotyping-by-sequencing (GBS). Loci-based association analysis detected 37 significant loci for the 17 traits. Thirty-seven identified candidate genes were involved in many biological processes. One single nucleotide polymorphism (SNP) (Chr1_140105435 A > T) located in the intron of the ATPase phospholipid transporting 11A gene (ATP11A) attained genome-wide significance associated with five weight traits. Eight SNPs were significantly associated with three body size traits, including the candidate gene plexin domain containing 2 (PLXDC2) associated with breast width and tensin 3 (TNS3) associated with fossil bone length. Only two SNPs were significantly associated with foot weight and four SNPs were significantly associated with heart weight. In the gene-based analysis, three genes (LOC101791418, TUBGCP3 (encoding tubulin gamma complex-associated protein 3), and ATP11A) were associated with four traits (42-day body weight, eviscerated weight, half-eviscerated weight, and leg muscle weight percentage). However, no loci were significantly associated with leg muscle weight in this study. Conclusions The novel results of this study improve our understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks. Electronic supplementary material The online version of this article (10.1186/s12864-018-5379-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng-Ting Deng
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, Beijing, 100107, China
| | - Fang-Xi Yang
- Beijing Golden Star Duck Co., LTD, Beijing, 100076, China
| | - Jin-Ping Hao
- Beijing Golden Star Duck Co., LTD, Beijing, 100076, China
| | - Si-Rui Chen
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
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10
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Yang L, Mo C, Shen W, Du X, Akbar Bhuiyan A, Li L, Li N, Gong Y, Li S. The recessive C locus in the MITF gene plays a key regulatory role in the plumage colour pattern of duck (Anas platyrhynchos). Br Poult Sci 2019; 60:105-108. [PMID: 30595026 DOI: 10.1080/00071668.2018.1564237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
1. The c/c alleles are responsible for the white plumage colour of ducks; however, the gene corresponding to this locus is still unclear. In order to identify the locus-related candidate gene associated with duck's plumage colour pattern, it was necessary to analyse the whole genome resequencing data. 2. A total of 929,465 SNPs in chromosome 13 and 1,688 SNPs in the region of the Microphthalmia-Associated Transcription Factor (MITF) gene were identified from whole genome resequencing data analysis. After construction of an FST plot from chromosome 13, MITF was highlighted as a candidate gene, possessing the highest FST value (0.811) on chromosome 13. 3. Six novel SNPs were discovered, located in the intronic region of the MITF gene. F2 progeny of Kaiya × Liancheng ducks (N = 1,061) were selected for genotyping by the Restriction Fragment Length Polymorphism (RFLP) technique. Association analysis using Haploview software was used for validation of the results. 4. Association results between SNPs and phenotypes showed significant association with corresponding phenotypes. All the significantly associated SNPs were located in the identified candidate gene. 5. The identified candidate gene provided novel information which is important in marker-assisted selection and breeding of duck and for the investigation of the C locus recessive white genetic mechanisms underlying plumage colour pattern.
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Affiliation(s)
- L Yang
- a Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education , Huazhong Agricultural University , Wuhan , Hubei Province , China
| | - C Mo
- a Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education , Huazhong Agricultural University , Wuhan , Hubei Province , China
| | - W Shen
- b Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics , Huazhong Agricultural University , Wuhan , China
| | - X Du
- b Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics , Huazhong Agricultural University , Wuhan , China
| | - A Akbar Bhuiyan
- a Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education , Huazhong Agricultural University , Wuhan , Hubei Province , China.,c Biotechnology Division , Bangladesh Livestock Research Institute , Dhaka , Bangladesh
| | - L Li
- d College of Biological Science and Technology , Hubei University for Nationalities , Enshi Hubei Province , China
| | - N Li
- a Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education , Huazhong Agricultural University , Wuhan , Hubei Province , China
| | - Y Gong
- a Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education , Huazhong Agricultural University , Wuhan , Hubei Province , China
| | - S Li
- a Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education , Huazhong Agricultural University , Wuhan , Hubei Province , China
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11
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Fan W, Xu L, Cheng H, Li M, Liu H, Jiang Y, Guo Y, Zhou Z, Hou S. Characterization of Duck ( Anas platyrhynchos) Short Tandem Repeat Variation by Population-Scale Genome Resequencing. Front Genet 2018; 9:520. [PMID: 30425731 PMCID: PMC6218588 DOI: 10.3389/fgene.2018.00520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/15/2018] [Indexed: 12/30/2022] Open
Abstract
Short tandem repeats (STRs) are usually associated with genetic diseases and gene regulatory functions, and are also important genetic markers for analysis of evolutionary, genetic diversity and forensic. However, for the majority of STRs in the duck genome, their population genetic properties and functional impacts remain poorly defined. Recent advent of next generation sequencing (NGS) has offered an opportunity for profiling large numbers of polymorphic STRs. Here, we reported a population-scale analysis of STR variation using genome resequencing in mallard and Pekin duck. Our analysis provided the first genome-wide duck STR reference including 198,022 STR loci with motif size of 2–6 base pairs. We observed a relatively uneven distribution of STRs in different genomic regions, which indicates that the occurrence of STRs in duck genome is not random, but undergoes a directional selection pressure. Using genome resequencing data of 23 mallard and 26 Pekin ducks, we successfully identified 89,891 polymorphic STR loci. Intensive analysis of this dataset suggested that shorter repeat motif, longer reference tract length, higher purity, and residing outside of a coding region are all associated with an increase in STR variability. STR genotypes were utilized for population genetic analysis, and the results showed that population structure and divergence patterns among population groups can be efficiently captured. In addition, comparison between Pekin duck and mallard identified 3,122 STRs with extremely divergent allele frequency, which overlapped with a set of genes related to nervous system, energy metabolism and behavior. The evolutionary analysis revealed that the genes containing divergent STRs may play important roles in phenotypic changes during duck domestication. The variation analysis of STRs in population scale provides valuable resource for future study of genetic diversity and genome evolution in duck.
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Affiliation(s)
- Wenlei Fan
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingyang Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hehe Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jiang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengkui Zhou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuisheng Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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12
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An intercross population study reveals genes associated with body size and plumage color in ducks. Nat Commun 2018; 9:2648. [PMID: 30018292 PMCID: PMC6050300 DOI: 10.1038/s41467-018-04868-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/31/2018] [Indexed: 12/15/2022] Open
Abstract
Comparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype-phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.
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13
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O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat Commun 2018; 9:1883. [PMID: 29784931 PMCID: PMC5962605 DOI: 10.1038/s41467-018-04267-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 01/07/2023] Open
Abstract
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning. Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.
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Affiliation(s)
- Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Paul M Barrett
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | | | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, IA, 50011, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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14
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Perelman PL, Pichler R, Gaggl A, Larkin DM, Raudsepp T, Alshanbari F, Holl HM, Brooks SA, Burger PA, Periasamy K. Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000 RAD and 15000 RAD. Sci Rep 2018; 8:1982. [PMID: 29386528 PMCID: PMC5792482 DOI: 10.1038/s41598-018-20223-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.
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Affiliation(s)
- Polina L Perelman
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
- Institute of Molecular and Cellular Biology and Novosibirsk State University, Novosibirsk, Russia
| | - Rudolf Pichler
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Anna Gaggl
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | | | | | | | | | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni, Vienna, Austria
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria.
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15
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Looi QH, Amin H, Aini I, Zuki M, Omar AR. De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird's nest producing swiftlets. BMC Genomics 2017; 18:504. [PMID: 28673247 PMCID: PMC5496224 DOI: 10.1186/s12864-017-3861-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Edible bird's nest (EBN), produced from solidified saliva secretions of specific swiftlet species during the breeding season, is one of the most valuable animal by-products in the world. The composition and medicinal benefits of EBN have been extensively studied, however, genomic and transcriptomic studies of the salivary glands of these birds have not been conducted. RESULTS The study described the transcriptomes of salivary glands from three swiftlet species (28 samples) generated by RNASeq. A total of 14,835 annotated genes and 428 unmapped genes were cataloged. The current study investigated the genes and pathways that are associated with the development of salivary gland and EBN composition. Differential expression and pathway enrichment analysis indicated that the expression of CREB3L2 and several signaling pathways involved in salivary gland development, namely, the EGFR, BMP, and MAPK signaling pathways, were up-regulated in swiftlets producing white EBN (Aerodramus fuciphagus) and black EBN (Aerodramus maximus) compared with non-EBN-producing swiftlets (Apus affinis). Furthermore, MGAT, an essential gene for the biosynthesis of N-acetylneuraminic acid (sialic acid), was highly expressed in both white- and black-nest swiftlets compared to non-EBN-producing swiftlets. Interspecies comparison between Aerodramus fuciphagus and Aerodramus maximus indicated that the genes involved in N-acetylneuraminic and fatty acid synthesis were up-regulated in Aerodramus fuciphagus, while alanine and aspartate synthesis pathways were up-regulated in Aerodramus maximus. Furthermore, gender-based analysis revealed that N-glycan trimming pathway was significantly up-regulated in male Aerodramus fuciphagus from its natural habitat (cave) compared to their female counterpart. CONCLUSIONS Transcriptomic analysis of salivary glands of different swiftlet species reveal differential expressions of candidate genes that are involved in salivary gland development and in the biosynthesis of various bioactive compounds found in EBN.
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Affiliation(s)
- Q H Looi
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - H Amin
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - I Aini
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - M Zuki
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - A R Omar
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. .,Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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16
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Lin R, Du X, Peng S, Yang L, Ma Y, Gong Y, Li S. Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos). Evol Bioinform Online 2015; 11:67-76. [PMID: 26819540 PMCID: PMC4721680 DOI: 10.4137/ebo.s21545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 12/21/2022] Open
Abstract
The duck is one of the most economically important waterfowl as a source of meat, eggs, and feathers. Characterizing the genetic variation in duck species is an important step toward linking genes or genomic regions with phenotypes. Human-driven selection during duck domestication and subsequent breed formation has likely left detectable signatures in duck genome. In this study, we employed a panel of >1.4 million single-nucleotide polymorphisms (SNPs) identified from the RNA sequencing (RNA-seq) data of 15 duck individuals. The density of the resulting SNPs is significantly positively correlated with the density of genes across the duck genome, which demonstrates that the usage of the RNA-seq data allowed us to enrich variant functional categories, such as coding exons, untranslated regions (UTRs), introns, and downstream/upstream. We performed a complete scan of selection signatures in the ducks using the composite likelihood ratio (CLR) and found 76 candidate regions of selection, many of which harbor genes related to phenotypes relevant to the function of the digestive system and fat metabolism, including TCF7L2, EIF2AK3, ELOVL2, and fatty acid-binding protein family. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to increase the known genetic information about this economically important animal.
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Affiliation(s)
- Ruiyi Lin
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaoyong Du
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.; College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Sixue Peng
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Liubin Yang
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yunlong Ma
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanzhang Gong
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shijun Li
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
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17
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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18
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Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014; 15:1060. [PMID: 25496766 PMCID: PMC4362836 DOI: 10.1186/1471-2164-15-1060] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
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Affiliation(s)
| | - Marta Farré
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Pamela E Lithgow
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Katie E Fowler
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
- />School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, Kent CT1 1QU UK
| | - Benjamin M Skinner
- />Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Rebecca O’Connor
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Gothami Fonseka
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Niclas Backström
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Yoichi Matsuda
- />Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810 Japan
| | - Peter Houde
- />Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA
| | - Erich D Jarvis
- />Department of Neurobiology, Duke University Medical Center, Box 3209, Durham, NC 27710 USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9PS UK
| | - Denis M Larkin
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Darren K Griffin
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
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19
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20
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Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes. Chromosome Res 2014; 22:85-97. [PMID: 24696127 DOI: 10.1007/s10577-014-9412-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Avian genome organisation is characterised, in part, by a set of microchromosomes that are unusually small in size and unusually large in number. Although containing about a quarter of the genome, they contain around half the genes and three quarters of the total chromosome number. Nonetheless, they continue to belie analysis by cytogenetic means. Chromosomal rearrangements play a key role in genome evolution, fertility and genetic disease and thus tools for analysis of the microchromosomes are essential to analyse such phenomena in birds. Here, we report the development of chicken microchromosomal paint pools, generation of pairs of specific microchromosome BAC clones in chicken, and computational tools for in silico comparison of the genomes of microchromosomes. We demonstrate the use of these molecular and computational tools across species, suggesting their use to generate a clear picture of microchromosomal rearrangements between avian species. With increasing numbers of avian genome sequences that are emerging, tools such as these will find great utility in assembling genomes de novo and for asking fundamental questions about genome evolution from a chromosomal perspective.
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Lee MO, Yang E, Morisson M, Vignal A, Huang YZ, Cheng HH, Muir WM, Lamont SJ, Lillehoj HS, Lee SH, Womack JE. Mapping and genotypic analysis of the NK-lysin gene in chicken. Genet Sel Evol 2014; 46:43. [PMID: 25001618 PMCID: PMC4120735 DOI: 10.1186/1297-9686-46-43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/13/2014] [Indexed: 11/10/2022] Open
Abstract
Background Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds. Results A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines. Conclusions The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - James E Womack
- Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA.
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