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Wu S, Dou T, Yuan S, Yan S, Xu Z, Liu Y, Jian Z, Zhao J, Zhao R, Zi X, Gu D, Liu L, Li Q, Wu DD, Jia J, Ge C, Su Z, Wang K. Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents. BMC Genomics 2024; 25:430. [PMID: 38693501 PMCID: PMC11061957 DOI: 10.1186/s12864-024-10316-z] [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: 12/04/2023] [Accepted: 04/16/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. RESULTS We identified varying numbers (17,497-17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 "missing" genes in birds in general, and 36 of the 174 "missing" genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. CONCLUSION The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.
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Affiliation(s)
- Siwen Wu
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sisi Yuan
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zonghui Jian
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rouhan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xiannian Zi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dahai Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Qihua Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
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2
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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [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: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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3
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Yin ZT, Li XQ, Sun YX, Smith J, Hincke M, Yang N, Hou ZC. Selection on the promoter regions plays an important role in complex traits during duck domestication. BMC Biol 2023; 21:303. [PMID: 38129834 PMCID: PMC10740227 DOI: 10.1186/s12915-023-01801-0] [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: 02/01/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the noncoding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood. RESULTS We constructed a genomics, transcriptomics, and epigenomics map of the duck genome and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the overexpression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment. CONCLUSIONS This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.
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Affiliation(s)
- Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, 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, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, 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
| | - Maxwell Hincke
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, 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, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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4
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Zhu F, Yin ZT, Zhao QS, Sun YX, Jie YC, Smith J, Yang YZ, Burt DW, Hincke M, Zhang ZD, Yuan MD, Kaufman J, Sun CJ, Li JY, Shao LW, Yang N, Hou ZC. A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 2023; 6:1233. [PMID: 38057566 PMCID: PMC10700341 DOI: 10.1038/s42003-023-05619-y] [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: 08/03/2022] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
A set of high-quality pan-genomes would help identify important genes that are still hidden/incomplete in bird reference genomes. In an attempt to address these issues, we have assembled a de novo chromosome-level reference genome of the Silkie (Gallus gallus domesticus), which is an important avian model for unique traits, like fibromelanosis, with unclear genetic foundation. This Silkie genome includes the complete genomic sequences of well-known, but unresolved, evolutionarily, endocrinologically, and immunologically important genes, including leptin, ovocleidin-17, and tumor-necrosis factor-α. The gap-less and manually annotated MHC (major histocompatibility complex) region possesses 38 recently identified genes, with differentially regulated genes recovered in response to pathogen challenges. We also provide whole-genome methylation and genetic variation maps, and resolve a complex genetic region that may contribute to fibromelanosis in these animals. Finally, we experimentally show leptin binding to the identified leptin receptor in chicken, confirming an active leptin ligand-receptor system. The Silkie genome assembly not only provides a rich data resource for avian genome studies, but also lays a foundation for further functional validation of resolved genes.
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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, 100193, Beijing, 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, 100193, Beijing, 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, 100193, Beijing, China
| | - Yun-Xiao Sun
- 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, 100193, Beijing, China
| | - Yu-Chen Jie
- 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, 100193, Beijing, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, 100101, Beijing, 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
| | - 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
| | - Zi-Ding Zhang
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Meng-Di Yuan
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Cong-Jiao Sun
- 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, 100193, Beijing, China
| | - Jun-Ying 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, 100193, Beijing, China
| | - Li-Wa Shao
- 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, 100193, Beijing, 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, 100193, Beijing, 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, 100193, Beijing, China.
- Sanya Institute of China Agricultural University, Beijing, China.
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5
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Gershman A, Hauck Q, Dick M, Jamison JM, Tassia M, Agirrezabala X, Muhammad S, Ali R, Workman RE, Valle M, Wong GW, Welch KC, Timp W. Genomic insights into metabolic flux in hummingbirds. Genome Res 2023; 33:703-714. [PMID: 37156619 PMCID: PMC10317124 DOI: 10.1101/gr.276779.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Hummingbirds are very well adapted to sustain efficient and rapid metabolic shifts. They oxidize ingested nectar to directly fuel flight when foraging but have to switch to oxidizing stored lipids derived from ingested sugars during the night or long-distance migratory flights. Understanding how this organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation. To explore these questions, we generated a chromosome-scale genome assembly of the ruby-throated hummingbird (A. colubris) using a combination of long- and short-read sequencing, scaffolding it using existing assemblies. We then used hybrid long- and short-read RNA sequencing of liver and muscle tissue in fasted and fed metabolic states for a comprehensive transcriptome assembly and annotation. Our genomic and transcriptomic data found positive selection of key metabolic genes in nectivorous avian species and deletion of critical genes (SLC2A4, GCK) involved in glucostasis in other vertebrates. We found expression of a fructose-specific version of SLC2A5 putatively in place of insulin-sensitive SLC2A5, with predicted protein models suggesting affinity for both fructose and glucose. Alternative isoforms may even act to sequester fructose to preclude limitations from transport in metabolism. Finally, we identified differentially expressed genes from fasted and fed hummingbirds, suggesting key pathways for the rapid metabolic switch hummingbirds undergo.
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Affiliation(s)
- Ariel Gershman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Quinn Hauck
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Morag Dick
- Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Jerrica M Jamison
- Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Michael Tassia
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xabier Agirrezabala
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Saad Muhammad
- Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Raafay Ali
- Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Rachael E Workman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Mikel Valle
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| | - G William Wong
- Department of Physiology and Center for Metabolism and Obesity Research, School of Medicine, The Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Kenneth C Welch
- Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21287, USA
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6
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Joyce W. Evolutionary loss of the ß1-adrenergic receptor in salmonids. Gen Comp Endocrinol 2023; 338:114279. [PMID: 37019291 DOI: 10.1016/j.ygcen.2023.114279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023]
Abstract
Whole-genome duplications (WGDs) have been at the heart of the diversification of ß-adrenergic receptors (ß-ARs) in vertebrates. Non-teleost jawed vertebrates typically possess three ß-AR genes: adrb1 (ß1-AR), adrb2 (ß2-AR), and adrb3 (ß3-AR), originating from the ancient 2R (two rounds) WGDs. Teleost fishes, owing to the teleost-specific WGD, have five ancestral adrb paralogs (adrb1, adrb2a, adrb2b, adrb3a and adrb3b). Salmonids are particularly intriguing from an evolutionary perspective as they experienced an additional WGD after separating from other teleosts. Moreover, adrenergic regulation in salmonids, especially rainbow trout, has been intensively studied for decades. However, the repertoire of adrb genes in salmonids has not been yet characterized. An exhaustive genome survey of diverse salmonids, spanning five genera, complemented by phylogenetic sequence analysis, revealed each species has seven adrb paralogs: two adrb2a, two adrb2b, two adrb3a and one adrb3b. Surprisingly, salmonids emerge as the first known jawed vertebrate lineage to lack adrb1. adrb1 is nevertheless highly expressed in the hearts of non-salmonid teleosts, indicating that the wealth of data on adrenergic regulation in salmonids should be generalised to other teleost fishes with caution. It is hypothesised that the loss of adrb1 could have been viable because of the evolutionary radiation of adrb2 and adrb3 genes attributable to the salmonid WGD.
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Affiliation(s)
- William Joyce
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark; Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, United Kingdom.
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7
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Luo P, Wang Z, Su C, Li H, Zhang H, Huang Y, Chen W. Chicken GLUT4 undergoes complex alternative splicing events and its expression in striated muscle changes dramatically during development. Poult Sci 2022; 102:102403. [PMID: 36584419 PMCID: PMC9827075 DOI: 10.1016/j.psj.2022.102403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Glucose transporter protein 4 (GLUT4) plays an important role in regulating insulin-mediated glucose homeostasis in mammals. Until now, studies on GLUT4 have focused on mammals mostly, while chicken GLUT4 has been rarely investigated. In this study, chicken GLUT4 mRNA sequences were obtained by combining conventional amplification, 5'- and 3'- rapid amplification of cDNA ends technique (RACE), then bioinformatics analysis on its genomic structure, splicing pattern, subcellular localization prediction and homologous comparisons were carried out. In addition, the distribution of GLUT4 was detected by RT-qPCR in bird's liver and striated muscles (cardiac muscle, pectoralis and leg muscle) at different ages, including embryonic day 14 (E14), E19, 7-day-old (D7), D21 and D49 (n = 3-4). Results showed that chicken GLUT4 gene produced at least 14 transcripts (GenBank accession No: OP491293-OP491306) through alternative splicing and polyadenylation, which predicted encoding 12 types of amino acid (AA) sequences (with length ranged from 65 AA to 519 AA). These proteins contain typical major facilitator superfamily domain of glucose transporters with length variations, sharing a common sequence of 59 AA, and were predicted to have distinct subcellular localization. The dominant transcript (named as T1) consists of 11 exons with an open reading frame being predicted encoding 519 AA. In addition, analyzing on the spatio-temporal expression of chicken GLUT4 showed it dominantly expressed in pectoralis, leg muscles and cardiac muscle, and the mRNA level of chicken GLUT4 dramatically fluctuated with birds' development in cardiac muscle, pectoralis and leg muscles, with the level at D21 significantly higher than that at E14, E19, and D49 (P < 0.05). These data indicated that chicken GLUT4 undergoes complex alternative splicing events, and GLUT4 expression level in striated muscle was subjected to dynamic regulation with birds' development. Results indicate these isoforms may play overlapping and distinct roles in chicken.
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Affiliation(s)
| | | | | | | | | | - Yanqun Huang
- College of Animal Science, Henan Agricultural University, Zhengzhou, 450000, China.
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8
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Wang F, Guo Y, Liu Z, Wang Q, Jiang Y, Zhao G. New insights into the novel sequences of the chicken pan-genome by liquid chip. J Anim Sci 2022; 100:6759641. [PMID: 36223424 PMCID: PMC9733507 DOI: 10.1093/jas/skac336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/11/2022] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence indicates that the missing sequences and genes in the chicken reference genome are involved in many crucial biological pathways, including metabolism and immunity. The low detection rate of novel sequences by resequencing hindered the acquisition of these sequences and the exploration of the relationship between new genes and economic traits. To improve the capture ratio of novel sequences, a 48K liquid chip including 25K from the reference sequence and 23K from the novel sequence was designed. The assay was tested on a panel of 218 animals from 5 chicken breeds. The average capture ratio of the reference sequence was 99.55%, and the average sequencing depth of the target sites was approximately 187X, indicating a good performance and successful application of liquid chips in farm animals. For the target region in the novel sequence, the average capture ratio was 33.15% and the average sequencing depth of target sites was approximately 60X, both of which were higher than that of resequencing. However, the different capture ratios and capture regions among varieties and individuals proved the difficulty of capturing these regions with complex structures. After genotyping, GWAS showed variations in novel sequences potentially relevant to immune-related traits. For example, a SNP close to the differentiation of lymphocyte-related gene IGHV3-23-like was associated with the H/L ratio. These results suggest that targeted capture sequencing is a preferred method to capture these sequences with complex structures and genes potentially associated with immune-related traits.
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Affiliation(s)
| | | | | | - Qiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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9
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Sweazea KL. Revisiting glucose regulation in birds - A negative model of diabetes complications. Comp Biochem Physiol B Biochem Mol Biol 2022; 262:110778. [PMID: 35817273 DOI: 10.1016/j.cbpb.2022.110778] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022]
Abstract
Birds naturally have blood glucose concentrations that are nearly double levels measured for mammals of similar body size and studies have shown that birds are resistant to insulin-mediated glucose uptake into tissues. While a combination of high blood glucose and insulin resistance is associated with diabetes-related pathologies in mammals, birds do not develop such complications. Moreover, studies have shown that birds are resistant to oxidative stress and protein glycation and in fact, live longer than similar-sized mammals. This review seeks to explore how birds regulate blood glucose as well as various theories that might explain their apparent resistance to insulin-mediated glucose uptake and adaptations that enable them to thrive in a state of relative hyperglycemia.
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10
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Brun A, Gutiérrez-Guerrero Y, Magallanes ME, Vidal EC, Karasov WH, Rio CMD. Opportunities lost? Evolutionary causes and ecological consequences of the absence of trehalose digestion in birds. Physiol Biochem Zool 2022; 95:340-349. [DOI: 10.1086/720232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Grosser S, Dutoit L, Foster Y, Robertson F, Fidler AE, Martini D, Knapp M, Robertson BC. Genomic evidence of a functional RH2 opsin in New Zealand parrots and implications for pest control. NEW ZEALAND JOURNAL OF ZOOLOGY 2022. [DOI: 10.1080/03014223.2022.2053554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Denise Martini
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Coastal People, Southern Skies Centre of Research Excellence, Department of Anatomy, University of Otago, Dunedin, New Zealand
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12
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Li M, Sun C, Xu N, Bian P, Tian X, Wang X, Wang Y, Jia X, Heller R, Wang M, Wang F, Dai X, Luo R, Guo Y, Wang X, Yang P, Hu D, Liu Z, Fu W, Zhang S, Li X, Wen C, Lan F, Siddiki AZ, Suwannapoom C, Zhao X, Nie Q, Hu X, Jiang Y, Yang N. De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on micro-chromosomes and sub-telomeric regions. Mol Biol Evol 2022; 39:6553873. [PMID: 35325213 PMCID: PMC9021737 DOI: 10.1093/molbev/msac066] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaomeng Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.,National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China
| | - Xinzheng Jia
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.,School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Mingshan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95064, USA
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Rongsong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiangnan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhenyu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shunjin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Fangren Lan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University, Chittagong-4202, Bangladesh
| | | | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Quebec, Canada
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
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13
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Burkhardt NB, Elleder D, Schusser B, Krchlíková V, Göbel TW, Härtle S, Kaspers B. The Discovery of Chicken Foxp3 Demands Redefinition of Avian Regulatory T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1128-1138. [PMID: 35173035 DOI: 10.4049/jimmunol.2000301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 12/17/2021] [Indexed: 11/19/2022]
Abstract
Since the publication of the first chicken genome sequence, we have encountered genes playing key roles in mammalian immunology, but being seemingly absent in birds. One of those was, until recently, Foxp3, the master transcription factor of regulatory T cells in mammals. Therefore, avian regulatory T cell research is still poorly standardized. In this study we identify a chicken ortholog of Foxp3 We prove sequence homology with known mammalian and sauropsid sequences, but also reveal differences in major domains. Expression profiling shows an association of Foxp3 and CD25 expression levels in CD4+CD25+ peripheral T cells and identifies a CD4-CD25+Foxp3high subset of thymic lymphocytes that likely represents yet undescribed avian regulatory T precursor cells. We conclude that Foxp3 is existent in chickens and that it shares certain functional characteristics with its mammalian ortholog. Nevertheless, pathways for regulatory T cell development and Foxp3 function are likely to differ between mammals and birds. The identification and characterization of chicken Foxp3 will help to define avian regulatory T cells and to analyze their functional properties and thereby advance the field of avian immunology.
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Affiliation(s)
- Nina B Burkhardt
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Daniel Elleder
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic; and
| | - Benjamin Schusser
- Reproductive Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Veronika Krchlíková
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic; and
| | - Thomas W Göbel
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Sonja Härtle
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Bernd Kaspers
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany;
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14
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots. Nat Commun 2022; 13:944. [PMID: 35177601 PMCID: PMC8854603 DOI: 10.1038/s41467-022-28585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots. Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.
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15
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Bravo GA, Schmitt CJ, Edwards SV. What Have We Learned from the First 500 Avian Genomes? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-085928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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16
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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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17
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Huttener R, Thorrez L, Veld TI, Granvik M, Van Lommel L, Waelkens E, Derua R, Lemaire K, Goyvaerts L, De Coster S, Buyse J, Schuit F. Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution. BMC Ecol Evol 2021; 21:176. [PMID: 34537008 PMCID: PMC8449477 DOI: 10.1186/s12862-021-01905-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/31/2021] [Indexed: 11/29/2022] Open
Abstract
Background Approximately 1000 protein encoding genes common for vertebrates are still unannotated in avian genomes. Are these genes evolutionary lost or are they not yet found for technical reasons? Using genome landscapes as a tool to visualize large-scale regional effects of genome evolution, we reexamined this question. Results On basis of gene annotation in non-avian vertebrate genomes, we established a list of 15,135 common vertebrate genes. Of these, 1026 were not found in any of eight examined bird genomes. Visualizing regional genome effects by our sliding window approach showed that the majority of these "missing" genes can be clustered to 14 regions of the human reference genome. In these clusters, an additional 1517 genes (often gene fragments) were underrepresented in bird genomes. The clusters of “missing” genes coincided with regions of very high GC content, particularly in avian genomes, making them “hidden” because of incomplete sequencing. Moreover, proteins encoded by genes in these sequencing refractory regions showed signs of accelerated protein evolution. As a proof of principle for this idea we experimentally characterized the mRNA and protein products of four "hidden" bird genes that are crucial for energy homeostasis in skeletal muscle: ALDOA, ENO3, PYGM and SLC2A4. Conclusions A least part of the “missing” genes in bird genomes can be attributed to an artifact caused by the difficulty to sequence regions with extreme GC% (“hidden” genes). Biologically, these “hidden” genes are of interest as they encode proteins that evolve more rapidly than the genome wide average. Finally we show that four of these “hidden” genes encode key proteins for energy metabolism in flight muscle. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01905-7.
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Affiliation(s)
- R Huttener
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - L Thorrez
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium.,Tissue Engineering Laboratory, Department of Development and Regeneration, KU Leuven Campus Kulak, Kortrijk, Belgium
| | - T In't Veld
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - M Granvik
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - L Van Lommel
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - E Waelkens
- Laboratory of Protein Phosphorylation and Proteomics, KU Leuven, Leuven, Belgium
| | - R Derua
- Laboratory of Protein Phosphorylation and Proteomics, KU Leuven, Leuven, Belgium
| | - K Lemaire
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - L Goyvaerts
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - S De Coster
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium
| | - J Buyse
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - F Schuit
- Gene Expression Unit, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, bus 901, 3000, Leuven, Belgium.
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18
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Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
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19
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Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
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Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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20
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Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature 2021; 592:737-746. [PMID: 33911273 PMCID: PMC8081667 DOI: 10.1038/s41586-021-03451-0] [Citation(s) in RCA: 773] [Impact Index Per Article: 257.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023]
Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA, USA
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcela Uliano-Silva
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mark Chaisson
- University of Southern California, Los Angeles, CA, USA
| | - Gregory L Gedman
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Iliana Bista
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center, Dresden, Germany
| | - Sadye Paez
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, University of St Andrews, St Andrews, UK
| | - Tanya M Lama
- University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA
| | - Frank Grutzner
- School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Dave Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Julia M George
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Bruce Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - George Turner
- School of Natural Sciences, Bangor University, Gwynedd, UK
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Maximilian Wagner
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | | | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic, Ivanić-Grad, Croatia
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Santa Cruz, CA, USA
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jay Ghurye
- Dovetail Genomics, Santa Cruz, CA, USA
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | - Dengfeng Guan
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA
| | - David F Clayton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, Qatar
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | | | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Frankfurt, Germany
| | | | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Woori Kwak
- eGnome, Inc., Seoul, Republic of Korea
- Hoonygen, Seoul, Korea
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Luis Nassar
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Federica Di Palma
- Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Tandy Warnow
- Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Oliver A Ryder
- San Diego Zoo Global, Escondido, CA, USA
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Stephen J O'Brien
- Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA, USA
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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21
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Mikalsen SO, í Kongsstovu S, Tausen M. Connexins during 500 Million Years-From Cyclostomes to Mammals. Int J Mol Sci 2021; 22:1584. [PMID: 33557313 PMCID: PMC7914757 DOI: 10.3390/ijms22041584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
It was previously shown that the connexin gene family had relatively similar subfamily structures in several vertebrate groups. Still, many details were left unclear. There are essentially no data between tunicates, which have connexins that cannot be divided into the classic subfamilies, and teleosts, where the subfamilies are easily recognized. There are also relatively few data for the groups that diverged between the teleosts and mammals. As many of the previously analyzed genomes have been improved, and many more genomes are available, we reanalyzed the connexin gene family and included species from all major vertebrate groups. The major results can be summarized as follows: (i) The same connexin subfamily structures are found in all Gnathostomata (jawed vertebrates), with some variations due to genome duplications, gene duplications and gene losses. (ii) In contrast to previous findings, birds do not have a lower number of connexins than other tetrapods. (iii) The cyclostomes (lampreys and hagfishes) possess genes in the alpha, beta, gamma and delta subfamilies, but only some of the genes show a phylogenetic affinity to specific genes in jawed vertebrates. Thus, two major evolutionary transformations have occurred in this gene family, from tunicates to cyclostomes and from cyclostomes to jawed vertebrates.
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Affiliation(s)
- Svein-Ole Mikalsen
- Faculty of Science and Technology, University of Faroe Islands, FO-100 Tórshavn, Faroe Islands; (S.í.K.); (M.T.)
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22
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Zhang F, Yin ZT, Zhang JF, Zhu F, Hincke M, Yang N, Hou ZC. Integrating transcriptome, proteome and QTL data to discover functionally important genes for duck eggshell and albumen formation. Genomics 2020; 112:3687-3695. [PMID: 32334113 DOI: 10.1016/j.ygeno.2020.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/28/2020] [Accepted: 04/20/2020] [Indexed: 12/20/2022]
Abstract
Duck egg quality improvement is an essential target for Asian poultry breeding. In total, 15 RNA-Seq libraries (magnum, isthmus, and uterus at two different physiological states) were sequenced from 48 weeks old Pekin ducks. De novo assembly and annotation methods were utilized to generate new reference transcripts. Our results revealed that 1264 and 2517 genes were differentially expressed in magnum and uterus in the presence versus absence of an egg, respectively. We identified 1089 genes that were differentially expressed in isthmus compared to uterus (in both presence and absence of a calcifying egg). We observed that 11 common DEGs were detected in the egg white proteomes of 6 different bird species including domestic Chicken, Duck, Goose, Turkey, Quail, and Pigeon. On the other hand, only one of the top five most highly expressed genes in duck isthmus was in this category for the chicken isthmus (SPINK7). Among the large number of DEGs during eggshell formation in ducks, only 41 genes showed a similar differential expression pattern in both duck and chicken. By combining chicken QTL database, chicken oviduct transcriptome and egg proteome data for five bird species, we have obtained high-quality gene lists for egg formation. This is the first study to elucidate the transcriptomic changes in different duck oviduct segments during egg formation, and to integrate QTL, proteome and transcriptome data to probe the functional genes associated with albumen secretion and eggshell mineralization.
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Affiliation(s)
- Fan Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jin-Feng Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - 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
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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23
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Elleder D, Kaspers B. After TNF-α, still playing hide-and-seek with chicken genes. Poult Sci 2020; 98:4373-4374. [PMID: 31189184 DOI: 10.3382/ps/pez307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Daniel Elleder
- Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Bernd Kaspers
- Department of Veterinary Science, Ludwig-Maximilians-Universität, 80539 Munich, Germany
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24
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Yin Z, Zhang F, Smith J, Kuo R, Hou ZC. Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. Sci Data 2019; 6:275. [PMID: 31754106 PMCID: PMC6872741 DOI: 10.1038/s41597-019-0293-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/31/2019] [Indexed: 01/05/2023] Open
Abstract
Duck (Anas platyrhynchos), one of the most economically important waterfowl, is an ideal model for studying the immune protection mechanism of birds. An incomplete duck reference genome and very limited availability of full-length cDNAs has hindered the identification of alternatively spliced transcripts and slowed down many basic studies in ducks. We applied PacBio Iso-Seq technologies to multiple tissues from duck for use in transcriptome sequencing. We obtained 199,993 full-length transcripts and comprehensively annotated these transcripts. 23,755 lncRNAs were predicted from all identified transcripts and 35,031 alternative splicing events, which divided into 5 models, were accurately predicted from 3,346 genes. Our data constitute a large increase in the known number of both lncRNA, and alternatively spliced transcripts of duck and plays an important role in improving current genome annotation. In addition, the data will be extremely useful for functional studies in other birds.
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Affiliation(s)
- ZhongTao Yin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Richard Kuo
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zhuo-Cheng Hou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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25
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Friedman-Einat M, Seroussi E. Avian Leptin: Bird's-Eye View of the Evolution of Vertebrate Energy-Balance Control. Trends Endocrinol Metab 2019; 30:819-832. [PMID: 31699239 DOI: 10.1016/j.tem.2019.07.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/13/2019] [Accepted: 07/08/2019] [Indexed: 12/20/2022]
Abstract
Discovery of the satiety hormone leptin in 1994 and its characterization in mammals provided a key tool to deciphering the complex mechanism governing adipose tissue regulation of appetite and energy expenditure. Surprisingly, despite the perfectly logical notion of an energy-storing tissue announcing the amount of fat stores using leptin signaling, alternate mechanisms were chosen in bird evolution. This conclusion emerged based on the recent discovery and characterization of genuine avian leptin - after it had been assumed missing by some, and erroneously identified by others. Critical evaluation of the past and present indications of the role of leptin in Aves provides a new perspective on the evolution of energy-balance control in vertebrates; proposing a regulation strategy alternative to the adipostat mechanism.
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Affiliation(s)
- Miriam Friedman-Einat
- Department of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeTsiyon, Israel.
| | - Eyal Seroussi
- Department of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeTsiyon, Israel
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26
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Wu C, Lv C, Wan Y, Li X, Zhang J, Li J, Wang Y. Arginine vasotocin (AVT)/mesotocin (MT) receptors in chickens: Evidence for the possible involvement of AVT-AVPR1 signaling in the regulation of oviposition and pituitary prolactin expression. Gen Comp Endocrinol 2019; 281:91-104. [PMID: 31121165 DOI: 10.1016/j.ygcen.2019.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 12/16/2022]
Abstract
Two structurally related peptides, arginine vasotocin (AVT) and mesotocin (MT), are reported to regulate many physiological processes, such as anti-diuresis and oviposition in birds, and their actions are likely mediated by four AVT/MT receptors (AVPR1A, AVPR1B, MTR and AVPR2b), which are orthologous/paralogous to human AVPR1A, AVPR1B, OXTR and AVPR2 respectively. However, our knowledge regarding the functions of these avian AVT/MT receptors has been limited. Here, we examined the functionality and expression of these receptors in chickens and investigated the roles of AVT in the anterior pituitary. Our results showed that 1) AVPR1A, AVPR1B and AVPR2b could be preferentially activated by AVT, monitored by cell-based luciferase reporter assays and/or Western blot, indicating that they are AVT-specific receptors (AVPR1A; AVPR1B) or AVT-preferring receptor (AVPR2b) functionally coupled to intracellular calcium, MAPK/ERK and cAMP/PKA signaling pathways. In contrast, MTR could be activated by AVT and MT with similar potencies, indicating that MTR is a receptor common for both peptides; 2) Using qPCR, differential expression of the four receptors was found in chicken tissues including the oviduct and anterior pituitary. In particular, only AVPR1A is abundantly expressed in the uterus, suggesting its involvement in mediating AVT-induced oviposition. 3) In cultured chick pituitary cells, AVT could stimulate ACTH and PRL expression and secretion, an action likely mediated by AVPR1B and/or AVPR1A abundantly expressed in anterior pituitary. Collectively, our data helps to elucidate the roles of AVT/MT in birds, such as the 'oxytocic action' of AVT, which induces uterine muscle contraction during oviposition.
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Affiliation(s)
- Chao Wu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Can Lv
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yiping Wan
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Xiaoxiao Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Jiannan Zhang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| | - Juan Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yajun Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
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