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Zhang R, Mu C, Chang L, Shen X, Bu Z, Yang M, Fu S, Tang Q, Liu P, Yang X. Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon. Animals (Basel) 2024; 14:1047. [PMID: 38612286 PMCID: PMC11011069 DOI: 10.3390/ani14071047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.
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Affiliation(s)
- Rui Zhang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Chunyu Mu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Lingling Chang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Xinyue Shen
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Zhu Bu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Mingjun Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Shengyong Fu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Qingping Tang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Peiyao Liu
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Xiaoming Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
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2
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Wang Y, Wang S, Gao Y, Li H, He X, Wang W, Ba Y, Wang L, Jiang J. An approach to rapidly identify the gender of the pigeon by using cross-priming amplification with immune-chromatographic strip. Talanta 2024; 269:125452. [PMID: 38064932 DOI: 10.1016/j.talanta.2023.125452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/20/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Most birds are monomorphic species and breeds, which makes it difficult to determine their gender by appearances, especially the pigeon is a farm animal with economic interest in meat production, ornamentals, sports, and experimental animals. Until now, the available methods for determining the gender of pigeons have mainly consisted of endoscopy, laparoscopy, karyotyping, polymerase chain reaction (PCR), and other similar techniques. Nonetheless, these methods have notable limitations, such as high expenses, invasiveness, and time-consuming procedures, which hinder their practicality for efficiently determining the gender of pigeons. Therefore, an easy, accurate, sensitive, on-site, affordable, and applicable rapid identification of the gender of the pigeon is widely needed for the owner of the pigeon. The purpose of this study was to develop and evaluate the efficacy of Cross-priming amplification (CPA) combined with an immune-chromatographic strip (CPA-strip) for gender identification of the pigeon. The methodology was optimized through various experimental trials. Subsequently, ten samples collected from pigeons were subjected to analysis using the optimized CPA-strip assay, and the results indicated that all female samples were accurately detected. In contrast, the blood samples collected from chickens and ducks were negative when tested with the CPA-strip assay. In conclusion, our study demonstrates the successful establishment of an immune-chromatographic CPA-strip assay for the on-site gender determination of pigeons with high accuracy.
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Affiliation(s)
- Yimin Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China.
| | - Shan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Yilin Gao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Hanglin Li
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Xun He
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Yierta Ba
- Inner Mongolia Autonomous Region Animal Disease Prevention and Control Center, Tongliao, Inner Mongolia, 028000, PR China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China.
| | - Jinqing Jiang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China.
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3
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Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid. G3 (BETHESDA, MD.) 2024; 14:jkad280. [PMID: 38066578 PMCID: PMC10849363 DOI: 10.1093/g3journal/jkad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
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Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA 94025, USA
- Digital BioLogic d.o.o, Ivanić-Grad 10310, Croatia
| | - Anna I Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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4
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Nannan M, Wenjun W, Ran Z, Yongsheng S, Rongyan Z, Hui C, Sumin Z, Hui X. Population genomics reveals that a missense mutation in EDNRB2 contributes to white plumage color in pigeons. Poult Sci 2024; 103:103225. [PMID: 38035860 PMCID: PMC10698677 DOI: 10.1016/j.psj.2023.103225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
Plumage color is an important economic trait for breed feature identification and consumer's requirements in pigeons. The domestic pigeon has multiple types of plumage color, thereby providing a unique opportunity to identify the genetic basis of plumage coloration. White feather color is common for meat and medicinal use. To investigate the genetic variation associated with white plumage color in pigeons, we use genome resequencing and population genomics to identify the genomic regions with strong selective signature between pigeons with brown and white plumage color. Meanwhile, we obtained some candidate genes with melanin or melanosome biosynthesis in selected regions. Finally, we identified a missense mutation p.E256K in the EDNRB2 completely associated with white plumage color. These findings provide a basis for genetic variation in pigeons with plumage color phenotype.
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Affiliation(s)
- Mao Nannan
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Wang Wenjun
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhang Ran
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Sun Yongsheng
- Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhou Rongyan
- Hebei Agricultural University, Baoding, Hebei 071001, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China.
| | - Chen Hui
- Hebei Agricultural University, Baoding, Hebei 071001, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China
| | - Zang Sumin
- Hebei Agricultural University, Baoding, Hebei 071001, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China
| | - Xie Hui
- Fuping Xige Industrial Co., Ltd., Fuping, Hebei 073200, China; Research Institute of Meat Pigeon Industry Technology, Fuping, Hebei 073200, China
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5
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Hernández-Alonso G, Ramos-Madrigal J, van Grouw H, Ciucani MM, Cavill EL, Sinding MHS, Gopalakrishnan S, Pacheco G, Gilbert MTP. Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences. Mol Biol Evol 2023; 40:msad243. [PMID: 37950889 PMCID: PMC10667084 DOI: 10.1093/molbev/msad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023] Open
Abstract
The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
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Affiliation(s)
- Germán Hernández-Alonso
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, United Kingdom
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily Louisa Cavill
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - George Pacheco
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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6
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Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F 1 hybrid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561892. [PMID: 37873124 PMCID: PMC10592783 DOI: 10.1101/2023.10.11.561892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Anna I. Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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7
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Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. PLoS Genet 2023; 19:e1010880. [PMID: 37862332 PMCID: PMC10588866 DOI: 10.1371/journal.pgen.1010880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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8
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Guhlin J, Le Lec MF, Wold J, Koot E, Winter D, Biggs PJ, Galla SJ, Urban L, Foster Y, Cox MP, Digby A, Uddstrom LR, Eason D, Vercoe D, Davis T, Howard JT, Jarvis ED, Robertson FE, Robertson BC, Gemmell NJ, Steeves TE, Santure AW, Dearden PK. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol 2023; 7:1693-1705. [PMID: 37640765 DOI: 10.1038/s41559-023-02165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
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Affiliation(s)
- Joseph Guhlin
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Marissa F Le Lec
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand
| | - David Winter
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
- Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand
| | - Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Lydia R Uddstrom
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Tāne Davis
- Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand
| | - Jason T Howard
- Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA
- Mirxes, Cambridge, MA, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fiona E Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
| | - Peter K Dearden
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand.
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9
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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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10
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Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550625. [PMID: 37546953 PMCID: PMC10402103 DOI: 10.1101/2023.07.26.550625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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11
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Luo H, Jiang X, Li B, Wu J, Shen J, Xu Z, Zhou X, Hou M, Huang Z, Ou X, Xu L. A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes). Commun Biol 2023; 6:746. [PMID: 37463976 PMCID: PMC10354230 DOI: 10.1038/s42003-023-05137-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard.
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Affiliation(s)
- Haoran Luo
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Xinrui Jiang
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Boping Li
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jiexin Shen
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zaoxu Xu
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China
| | - Xiaoping Zhou
- Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Minghao Hou
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China
| | - Zhen Huang
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, 350108, China.
- Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Xiaobin Ou
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China.
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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12
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Haddock J, Domyan ET. A DNA Replication Mechanism Can Explain Structural Variation at the Pigeon Recessive Red Locus. Biomolecules 2022; 12:1509. [PMID: 36291717 PMCID: PMC9599118 DOI: 10.3390/biom12101509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 08/08/2023] Open
Abstract
For species to adapt to their environment, evolution must act upon genetic variation that is present in the population. Elucidating the molecular mechanisms that give rise to this variation is thus of crucial importance for understanding how organisms evolve. In addition to variation caused by point mutations, structural variation (deletions, duplications, inversions, translocations) is also an important source of variety. Mechanisms involving recombination, transposition and retrotransposition, and replication have been proposed for generating structural variation, and each are capable of explaining certain rearrangements. In this study, we conduct a detailed analysis of two partially overlapping rearrangements (e1 and e2 allele) in domestic rock pigeon (Columba livia) which are both associated with the recessive red phenotype. We find that a replicative mechanism is best able to explain the complex architecture of the e1 allele, and is also compatible with the simpler architecture of the e2 allele as well.
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Affiliation(s)
| | - Eric T. Domyan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
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13
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Kim JA, Choi BS, Kim NS, Kang SG, Park JY, Yeo YG, Bae JH, Lee JH, Um T, Choi IY, An J. Whole-genome sequencing revealed different demographic histories among the Korean endemic hill pigeon (Columba rupestris), rock pigeon (Columba livia var. domestica) and oriental turtle dove (Streptopelia orientalis). Genes Genomics 2022; 44:1231-1242. [PMID: 35951153 DOI: 10.1007/s13258-022-01288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/13/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. OBJECTIVES Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples. RESULTS The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased. CONCLUSION The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5-1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes.
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Affiliation(s)
- Jung A Kim
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Beom-Soon Choi
- Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea
| | - Nam-Soo Kim
- Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea
| | - Seung-Gu Kang
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang-gun, Republic of Korea
| | - Jin-Young Park
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Yong-Gu Yeo
- Conservation and Health Center, Seoul Zoo, Gwcheon, Republic of Korea
| | - Ju-Hee Bae
- Conservation and Health Center, Seoul Zoo, Gwcheon, Republic of Korea
| | - Ju-Hee Lee
- Conservation and Health Center, Seoul Zoo, Gwcheon, Republic of Korea
| | - Taeyoung Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - Ik-Young Choi
- Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea. .,Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea.
| | - Junghwa An
- National Institute of Biological Resources, Incheon, Republic of Korea.
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14
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Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, Lieberman Aiden E, Osipova E, Hiller M, Morales HE, Magrath MJL, Clarke RH, Sunnucks P, Pavlova A. Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater. Gigascience 2022; 11:giac025. [PMID: 35348671 PMCID: PMC8963300 DOI: 10.1093/gigascience/giac025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/13/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. RESULTS We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. CONCLUSIONS The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
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Affiliation(s)
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- GeneSEQ Sdn Bhd, 48300 Rawang, Selangor, Malaysia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth WA 6009,Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- UWA School of Agriculture and Environment, The University of Western Australia, Perth WA 6009,Australia
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 101307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 101307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Hernán E Morales
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Denmark
| | - Michael J L Magrath
- Department of Wildlife Conservation and Science, Zoos Victoria, Parkville, VIC 3052, Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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15
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Boyd BM, Nguyen NP, Allen JM, Waterhouse RM, Vo KB, Sweet AD, Clayton DH, Bush SE, Shapiro MD, Johnson KP. Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites. Proc Biol Sci 2022; 289:20220042. [PMID: 35259992 PMCID: PMC8905168 DOI: 10.1098/rspb.2022.0042] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Adaptive radiation is an important mechanism of organismal diversification and can be triggered by new ecological opportunities. Although poorly studied in this regard, parasites are an ideal group in which to study adaptive radiations because of their close associations with host species. Both experimental and comparative studies suggest that the ectoparasitic wing lice of pigeons and doves have adaptively radiated, leading to differences in body size and overall coloration. Here, we show that long-distance dispersal by dove hosts was central to parasite diversification because it provided new ecological opportunities for parasites to speciate after host-switching. We further show that among extant parasite lineages host-switching decreased over time, with cospeciation becoming the more dominant mode of parasite speciation. Taken together, our results suggest that host dispersal, followed by host-switching, provided novel ecological opportunities that facilitated adaptive radiation by parasites.
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Affiliation(s)
- Bret M Boyd
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Nam-Phuong Nguyen
- Department of Computer Science, University of Illinois, Champaign, IL, USA
| | - Julie M Allen
- Department of Biology, University of Nevada Reno, Reno, NV, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kyle B Vo
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
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16
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Maclary ET, Phillips B, Wauer R, Boer EF, Bruders R, Gilvarry T, Holt C, Yandell M, Shapiro MD. Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). Mol Biol Evol 2021; 38:5376-5390. [PMID: 34459920 PMCID: PMC8662629 DOI: 10.1093/molbev/msab260] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.
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Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tyler Gilvarry
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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17
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Boer EF, Van Hollebeke HF, Maclary ET, Holt C, Yandell M, Shapiro MD. A ROR2 coding variant is associated with craniofacial variation in domestic pigeons. Curr Biol 2021; 31:5069-5076.e5. [PMID: 34551284 PMCID: PMC8612976 DOI: 10.1016/j.cub.2021.08.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/01/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022]
Abstract
Vertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways.1,2 Within species, canalized development typically produces modest morphological variation. However, as a result of millennia of artificial selection, the domestic pigeon displays radical craniofacial variation within a single species. One of the most striking cases of pigeon craniofacial variation is the short-beak phenotype, which has been selected in numerous breeds. Classical genetic experiments suggest that pigeon beak length is regulated by a small number of genetic factors, one of which is sex linked (Ku2 locus).3-5 However, the genetic underpinnings of pigeon craniofacial variation remain unknown. Using geometric morphometrics and quantitative trait locus (QTL) mapping on an F2 intercross between a short-beaked Old German Owl (OGO) and a medium-beaked Racing Homer (RH), we identified a single Z chromosome locus that explains a majority of the variation in beak morphology in the F2 population. Complementary comparative genomic analyses revealed that the same locus is strongly differentiated between breeds with short and medium beaks. Within the Ku2 locus, we identified an amino acid substitution in the non-canonical Wnt receptor ROR2 as a putative regulator of pigeon beak length. The non-canonical Wnt pathway serves critical roles in vertebrate neural crest cell migration and craniofacial morphogenesis.6,7 In humans, ROR2 mutations cause Robinow syndrome, a congenital disorder characterized by skeletal abnormalities, including a widened and shortened facial skeleton.8,9 Our results illustrate how the extraordinary craniofacial variation among pigeons can reveal genetic regulators of vertebrate craniofacial diversity.
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Affiliation(s)
- Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
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18
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Sivalingam PN, Mahajan MM, Satheesh V, Chauhan S, Changal H, Gurjar K, Singh D, Bhan C, Sivalingam A, Marathe A, Ram C, Dokka N, More TA, Padaria JC, Bhat KV, Mohapatra T. Distinct morpho-physiological and biochemical features of arid and hyper-arid ecotypes of Ziziphus nummularia under drought suggest its higher tolerance compared with semi-arid ecotype. TREE PHYSIOLOGY 2021; 41:2063-2081. [PMID: 33929534 DOI: 10.1093/treephys/tpab058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Tree species in the arid and semi-arid regions use various strategies to combat drought stress. Ziziphus nummularia (Burm. f.) Wight et Arn., native to the Thar Desert in India, is highly drought-tolerant. To identify the most drought-tolerant ecotype of Z. nummularia, one ecotype each from semi-arid (Godhra, annual rainfall >750 mm), arid (Bikaner, 250-350 mm) and hyper-arid (Jaisalmer, <150 mm) regions was selected along with two other Ziziphus species, Ziziphus mauritiana Lamk. and Ziziphus rotundifolia Lamk., and screened for parameters contributing to drought tolerance. Among these, Z. nummularia (Jaisalmer) (CIAHZN-J) was the most drought - tolerant. The tolerance nature of CIAHZN-J was associated with increased membrane stability, root length and number, length of hairs and thorns, root dry/fresh weight ratio, seed germination (at -0.5 MPa), proline content (31-fold), catalase and sugar content (two- to three-fold). Apart from these characteristics, it also exhibited the longest duration to reach highest cumulative drought stress rating, maintained higher relative water content for a longer period of time with reduced leaf size, leaf rolling and falling of older leaves, and displayed sustained shoot growth during drought stress. To determine drought tolerance in Ziziphus, we developed a morphological symptom-based screening technique in this study. Additionally, transcriptome profiling of CIAHZN-J in response to drought revealed the up-regulation of genes involved in sugar metabolism and transport, abscisic acid biosynthesis, osmoregulation, reactive oxygen species homeostasis and maintaining water potential. Expression profiles and semi-quantitative reverse transcription PCR results further correlated with the physiological and biochemical mechanisms. In conclusion, CIAHZN-J is an excellent genetic stock for the identification of drought-responsive genes and can also be deployed in crop improvement programs for drought tolerance.
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Affiliation(s)
- P N Sivalingam
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - Mahesh M Mahajan
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - Viswanathan Satheesh
- ICAR-National Institute for Plant Biotechnology (Previously: National Research Centre on Plant Biotechnology), IARI Campus, PUSA, New Delhi, 110012, India
| | - Sarita Chauhan
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Harish Changal
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Karun Gurjar
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Dhurendra Singh
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Chander Bhan
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Anandhan Sivalingam
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra 410 505, India
| | - Ashish Marathe
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Narasimham Dokka
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - T A More
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - J C Padaria
- ICAR-National Institute for Plant Biotechnology (Previously: National Research Centre on Plant Biotechnology), IARI Campus, PUSA, New Delhi, 110012, India
| | - K V Bhat
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, PUSA, New Delhi 110012, India
| | - T Mohapatra
- ICAR-National Institute for Plant Biotechnology (Previously: National Research Centre on Plant Biotechnology), IARI Campus, PUSA, New Delhi, 110012, India
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19
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Boer EF, Maclary ET, Shapiro MD. Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons. Evol Dev 2021; 23:477-495. [PMID: 34914861 PMCID: PMC9119316 DOI: 10.1111/ede.12395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/28/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
Deciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak shape, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.
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Affiliation(s)
- Elena F. Boer
- School of Biological SciencesUniversity of UtahSalt Lake CityUtahUSA
| | - Emily T. Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUtahUSA
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20
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Sjodin BMF, Galbreath KE, Lanier HC, Russello MA. Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps). J Hered 2021; 112:549-557. [PMID: 34036348 PMCID: PMC8558581 DOI: 10.1093/jhered/esab031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023] Open
Abstract
The American pika (Ochotona princeps) is an alpine lagomorph found throughout western North America. Primarily inhabiting talus slopes at higher elevations (>2000 m), American pikas are well adapted to cold, montane environments. Warming climates on both historical and contemporary scales have contributed to population declines in American pikas, positioning them as a focal mammalian species for investigating the ecological effects of climate change. To support and expand ongoing research efforts, here, we present a highly contiguous and annotated reference genome assembly for the American pika (OchPri4.0). This assembly was produced using Dovetail de novo proximity ligation methods and annotated through the NCBI Eukaryotic Genome Annotation pipeline. The resulting assembly was chromosome- scale, with a total length of 2.23 Gb across 9350 scaffolds and a scaffold N50 of 75.8 Mb. The vast majority (>97%) of the total assembly length was found within 36 large scaffolds; 33 of these scaffolds correlated to whole autosomes, while the X chromosome was covered by 3 large scaffolds. Additionally, we identified 17 enriched gene ontology terms among American pika-specific genes putatively related to adaptation to high-elevation environments. This high-quality genome assembly will serve as a springboard for exploring the evolutionary underpinnings of behavioral, ecological, and taxonomic diversification in pikas as well as broader-scale eco-evolutionary questions pertaining to cold-adapted species in general.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Hayley C Lanier
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, Canada
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21
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Esmailizadeh A, Kharrati-Koopaee H, Nanaei HA. Whole genome resequencing data for rock pigeon (Columba livia). BMC Res Notes 2021; 14:305. [PMID: 34372924 PMCID: PMC8351366 DOI: 10.1186/s13104-021-05718-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
Objective Navigation is the most important feature of homing pigeons, however no integrated response to genetic mechanism of navigation has been reported. The generated data herein represent whole-genome resequencing data for homing pigeon and three other breeds of rock pigeons. Selective sweep analysis between homing pigeon and other breeds of rock pigeon can provide new insight about identification of candidate genes and biological pathways for homing pigeon ability. Data description Whole-genomes sequence data related to 95 birds from four breeds of rock pigeons including, 29 feral pigeons, 24 Shiraz tumblers, 24 Persian high flyers and 18 homing pigeons were provided. More than 6.94 billion short reads with coverage (average ≈7.50 x) and 407.1 Gb data were produced. Whole genome sequencing was carried out on the Illumina Hiseq 2000 platform using a 350 bp library size and 150 bp paired-end read lengths. The whole genome sequencing data have been submitted at the NCBI SRA Database (PRJNA532675). The presented data set can provide useful genomic information to explain the genetic mechanism of navigation ability of homing pigeons and also testing other genetic hypothesis by genomic analysis.
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Affiliation(s)
- Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Hamed Kharrati-Koopaee
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran. .,Institute of Biotechnology, Shiraz University, Shiraz, Iran.
| | - Hojjat Assadoullahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
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22
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Si S, Xu X, Zhuang Y, Gao X, Zhang H, Zou Z, Luo SJ. The genetics and evolution of eye color in domestic pigeons (Columba livia). PLoS Genet 2021; 17:e1009770. [PMID: 34460822 PMCID: PMC8432899 DOI: 10.1371/journal.pgen.1009770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/10/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022] Open
Abstract
The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris colors exhibit striking interspecific and intraspecific variations that correspond to unique evolutionary and ecological histories. Here, we identified the genetic basis of pearl (white) iris color in domestic pigeons (Columba livia) to explore the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) approach in 92 pigeons, we mapped the pearl iris trait to a 9 kb region containing the facilitative glucose transporter gene SLC2A11B. A nonsense mutation (W49X) leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, thus resulting in the pearl iris phenotype. Coalescence and phylogenetic analyses indicated that the mutation originated approximately 5,400 years ago, coinciding with the onset of pigeon domestication, while positive selection was likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in six species from six distinct lineages, four of which associated with their signature brown or blue eyes and lack of pteridine. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that during and after avian divergence from the reptilian ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated in the presence of feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.
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Affiliation(s)
- Si Si
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaodong Gao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Zhengting Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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23
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Ragucci S, Acconcia C, Russo R, Landi N, Valletta M, Clemente A, Chambery A, Russo L, Di Maro A. Ca 2+ as activator of pseudoperoxidase activity of pigeon, Eurasian woodcock and chicken myoglobins: New features for meat preservation studies. Food Chem 2021; 363:130234. [PMID: 34126569 DOI: 10.1016/j.foodchem.2021.130234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
Myoglobin (Mb), hemeprotein that binds dioxygen in muscle, affects meat colour. Moreover, in presence of peroxides, metMb is a potent oxidant involved in oxidative rancidity in meat. Here, following pigeon Mb purification and primary structure mass spectroscopy characterization, we determined its autoxidation rate and pseudoperoxidase activity with respect to chicken and E. woodcock Mbs. The three Mbs exhibit different autoxidation rates (0.153-h-1 pigeon, 0.194-h-1 chicken and 0.220-h-1 E. woodcock Mbs) and similar specificity constant (9.86x103 M-1s-1 pigeon, 8.81x103 M-1s-1 chicken and 9.90x103 M-1s-1 E. woodcock Mbs), considering their pseudoperoxidase activity. Moreover, for the first time, we detected an increase in pseudoperoxidase activity in presence of Ca2+, particularly at pH 5.8. NMR and CD data indicate that the nonspecific Ca2+ binding induces small local structural rearrangements that in turn slightly reduce pigeon Mb thermal stability. However, considering Ca2+ concentration variations before and post-mortem, this finding must be considered for meat preservation.
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Affiliation(s)
- Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Clementina Acconcia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Angela Clemente
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Via Vivaldi 43, 81100-Caserta, Italy.
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24
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Pacheco G, van Grouw H, Shapiro MD, Gilbert MTP, Vieira FG. Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biol Evol 2021; 12:136-150. [PMID: 32053199 PMCID: PMC7144551 DOI: 10.1093/gbe/evaa027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.
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Affiliation(s)
- George Pacheco
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark.,The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, Hertfordshire, United Kingdom
| | | | - Marcus Thomas P Gilbert
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark.,The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Denmark.,NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Filipe Garrett Vieira
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark
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25
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Baldwin-Brown JG, Villa SM, Vickrey AI, Johnson KP, Bush SE, Clayton DH, Shapiro MD. The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite. G3 (BETHESDA, MD.) 2021; 11:jkab009. [PMID: 33604673 PMCID: PMC8022949 DOI: 10.1093/g3journal/jkab009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/13/2020] [Indexed: 01/01/2023]
Abstract
The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.
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Affiliation(s)
| | - Scott M Villa
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA 30322, USA
| | - Anna I Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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26
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Andrade P, Gazda MA, Araújo PM, Afonso S, Rasmussen JA, Marques CI, Lopes RJ, Gilbert. MTP, Carneiro M. Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates. PLoS Genet 2021; 17:e1009404. [PMID: 33621224 PMCID: PMC7935293 DOI: 10.1371/journal.pgen.1009404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/05/2021] [Accepted: 02/08/2021] [Indexed: 01/04/2023] Open
Abstract
Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Małgorzata A. Gazda
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Pedro M. Araújo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- MARE–Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Jacob. A. Rasmussen
- Center for Evolutionary Genomics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cristiana I. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Ricardo J. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - M. Thomas P. Gilbert.
- Center for Evolutionary Genomics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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27
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Carlen E, Munshi‐South J. Widespread genetic connectivity of feral pigeons across the Northeastern megacity. Evol Appl 2021; 14:150-162. [PMID: 33519962 PMCID: PMC7819573 DOI: 10.1111/eva.12972] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Urbanization may restrict, facilitate, or have no effect on gene flow, depending on the organism and extent of urbanization. In human commensals, with high dispersal ability, urbanization can facilitate gene flow by providing continuous suitable habitat across a wide range. Additionally, suburban or rural areas with lower human population density may act as a barrier to gene flow for these human commensals. Spatial population genetic approaches provide a means to understand genetic connectivity across geographically expansive areas that encompass multiple metropolitan areas. Here, we examined the spatial genetic patterns of feral pigeons (Columba livia) living in cities in the eastern United States. We focused our sampling on the Northeastern megacity, which is a region covering six large cities (Boston, Providence, New York City, Philadelphia, Baltimore, and Washington, DC). We performed ddRAD-Seqon 473 samples, recovered 35,200 SNPs, and then used multiple evolutionary clustering analyses to investigate population structuring. These analyses revealed that pigeons formed two genetic clusters-a northern cluster containing samples from Boston and Providence and a southern cluster containing all other samples. This substructuring is possibly due to reduced urbanization across coastal Connecticut that separates Boston and Providence from New York and mid-Atlantic cities. We found that pairs of pigeons within 25 km are highly related (Mantel r = 0.217, p = .001) and that beyond 50 km, pigeons are no more related than they would be at random. Our analysis detected higher-than-expected gene flow under an isolation by distance model within each city. We conclude that the extreme urbanization characteristic of the Northeastern megacity is likely facilitating gene flow in feral pigeons.
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28
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Yang J, Gu J, Hu Y, Wang N, Gao J, Wang P. Molecular cloning and characterization of HSP60 gene in domestic pigeons (Columba livia) and differential expression patterns under temperature stress. Cell Stress Chaperones 2021; 26:115-127. [PMID: 32880058 PMCID: PMC7736444 DOI: 10.1007/s12192-020-01160-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/19/2020] [Accepted: 08/25/2020] [Indexed: 12/21/2022] Open
Abstract
Heat shock protein 60 (HSP60) is a well-recognized multifunctional protein, playing a substantial role in protecting organisms from environmental stress. The domestic pigeon (Columba livia) is a promising model organism, with important economic and ecological value, and its health is susceptible to temperature stress. To explore the molecular characteristics, tissue expression profile, and response to temperature stress for HSP60 of Columba livia (ClHSP60), we firstly cloned and characterized the complete cDNA sequence and investigated its expression profile under optimal conditions and acute temperature stress. The cDNA of ClHSP60 contained 2257 nucleotides, consisting of 12 exons with length ranging from 65 to 590 bp. The open reading frame (ORF) encoded 573 amino acids with calculated molecular weight of 60.97 kDa that contained a number of structurally prominent domains or motifs. Under optimal temperature conditions, levels of ClHSP60 expression differed between all the tested tissues (the highest was noted in liver and the lowest in pectoralis major muscle). Under acute temperature stress, five patterns of change were detected in the tested tissues, suggesting that different tissues in domestic pigeons differentially responded to various temperature stress conditions. Upregulation of ClHSP60 expression was highest in the lung and pectoralis major muscle, reflecting the crucial role of these two tissues in temperature regulation. However, the crop, cerebrum, and heart showed little change or decreased ClHSP60 expression. The results indicate that ClHSP60 may be sensitive to and play pivotal roles in responding to acute temperature stress.
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Affiliation(s)
- Jianke Yang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- Research laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, China
| | - Juan Gu
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- School of pharmacy, Wannan Medical College, Wuhu, 241001, China
| | - Yuqing Hu
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, 241001, China
| | - Nan Wang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, 241001, China
| | - Jiguang Gao
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- Research laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, China
| | - Ping Wang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China.
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29
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Andrade P, Cataldo D, Fontaine R, Rodrigues TM, Queirós J, Neves V, Fonseca A, Carneiro M, Gonçalves D. Selection underlies phenotypic divergence in the insular Azores woodpigeon. ZOOL SCR 2020. [DOI: 10.1111/zsc.12456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pedro Andrade
- CIBIO‐InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Daniele Cataldo
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Rémi Fontaine
- CIBIO‐InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Tiago M. Rodrigues
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
- Direção Regional dos Recursos Florestais (DRRF) Azores Portugal
| | - João Queirós
- CIBIO‐InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Verónica Neves
- MARE, Marine & Environmental Sciences Centre Institute of Marine Research (IMAR) OKEANOS R&D Center Faculdade de Ciências e Tecnologia Universidade dos Açores Horta Portugal
| | - Amélia Fonseca
- Departamento de Biologia Faculdade de Ciências e Tecnologia Universidade dos Açores Azores Portugal
| | - Miguel Carneiro
- CIBIO‐InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - David Gonçalves
- CIBIO‐InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
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30
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Hochstoeger T, Al Said T, Maestre D, Walter F, Vilceanu A, Pedron M, Cushion TD, Snider W, Nimpf S, Nordmann GC, Landler L, Edelman N, Kruppa L, Dürnberger G, Mechtler K, Schuechner S, Ogris E, Malkemper EP, Weber S, Schleicher E, Keays DA. The biophysical, molecular, and anatomical landscape of pigeon CRY4: A candidate light-based quantal magnetosensor. SCIENCE ADVANCES 2020; 6:eabb9110. [PMID: 32851187 PMCID: PMC7423367 DOI: 10.1126/sciadv.abb9110] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
The biophysical and molecular mechanisms that enable animals to detect magnetic fields are unknown. It has been proposed that birds have a light-dependent magnetic compass that relies on the formation of radical pairs within cryptochrome molecules. Using spectroscopic methods, we show that pigeon cryptochrome clCRY4 is photoreduced efficiently and forms long-lived spin-correlated radical pairs via a tetrad of tryptophan residues. We report that clCRY4 is broadly and stably expressed within the retina but enriched at synapses in the outer plexiform layer in a repetitive manner. A proteomic survey for retinal-specific clCRY4 interactors identified molecules that are involved in receptor signaling, including glutamate receptor-interacting protein 2, which colocalizes with clCRY4. Our data support a model whereby clCRY4 acts as an ultraviolet-blue photoreceptor and/or a light-dependent magnetosensor by modulating glutamatergic synapses between horizontal cells and cones.
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Affiliation(s)
- Tobias Hochstoeger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Tarek Al Said
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Dante Maestre
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Florian Walter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Alexandra Vilceanu
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Miriam Pedron
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Thomas D. Cushion
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - William Snider
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Simon Nimpf
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Gregory Charles Nordmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Lukas Landler
- Institute of Zoology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Nathaniel Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Lennard Kruppa
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Stefan Schuechner
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna 1030, Austria
| | - Egon Ogris
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna 1030, Austria
| | - E. Pascal Malkemper
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Max Planck Research Group Neurobiology of Magnetoreception, Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, Bonn 53175, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - David A. Keays
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Australia
- Division of Neurobiology, Department Biology II, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
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31
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Nowoshilow S, Tanaka EM. Introducing www.axolotl-omics.org - an integrated -omics data portal for the axolotl research community. Exp Cell Res 2020; 394:112143. [PMID: 32540400 DOI: 10.1016/j.yexcr.2020.112143] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/31/2022]
Abstract
Genomic resources are indispensable for biological investigations in model organisms. In recent years, a number of genomic resources including a full genome assembly, extensive transcriptomic data, as well as genome editing has been developed for the axolotl, a classical model organism for developmental, neurobiological and regeneration studies, making the axolotl a highly versatile system. Here we describe the Axolotl-omics website that allows rapid ortholog searches, and access to genome and transcriptomic resources.
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Affiliation(s)
- Sergej Nowoshilow
- Institute of Molecular Pathology Vienna Biocenter, Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Elly M Tanaka
- Institute of Molecular Pathology Vienna Biocenter, Campus Vienna Biocenter 1, 1030, Vienna, Austria.
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32
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Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 2020; 16:e1008274. [PMID: 32433666 PMCID: PMC7239393 DOI: 10.1371/journal.pgen.1008274] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons. The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.
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Affiliation(s)
- Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Hannah Van Hollebeke
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward J. Osborne
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Zev Kronenberg
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Emily Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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33
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Jayakumar V, Ishii H, Seki M, Kumita W, Inoue T, Hase S, Sato K, Okano H, Sasaki E, Sakakibara Y. An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data. BMC Genomics 2020; 21:243. [PMID: 32241258 PMCID: PMC7114785 DOI: 10.1186/s12864-020-6657-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. RESULTS Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome. CONCLUSIONS Altogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data.
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Affiliation(s)
- Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Hiromi Ishii
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Misato Seki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Wakako Kumita
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821 Japan
| | - Takashi Inoue
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821 Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, 160-8582 Japan
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako-shi, Saitama, 351-0198 Japan
| | - Erika Sasaki
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821 Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
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34
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Ma H, Ni A, Ge P, Li Y, Shi L, Wang P, Fan J, Isa AM, Sun Y, Chen J. Analysis of Long Non-Coding RNAs and mRNAs Associated with Lactation in the Crop of Pigeons ( Columba livia). Genes (Basel) 2020; 11:genes11020201. [PMID: 32079139 PMCID: PMC7073620 DOI: 10.3390/genes11020201] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Pigeons have the ability to produce milk and feed their squabs. The genetic mechanisms underlying milk production in the crops of 'lactating' pigeons are not fully understood. In this study, RNA sequencing was employed to profile the transcriptome of lncRNA and mRNA in lactating and non-'lactating' pigeon crops. We identified 7066 known and 17,085 novel lncRNAs. Of these lncRNAs, 6166 were differentially expressed. Among the 15,138 mRNAs detected, 6483 were differentially expressed, including many predominant genes with known functions in the milk production of mammals. A GO annotation analysis revealed that these genes were significantly enriched in 55, 65, and 30 pathways of biological processes, cellular components, and molecular functions, respectively. A KEGG pathway enrichment analysis revealed that 12 pathways (involving 544 genes), including the biosynthesis of amino acids, the propanoate metabolism, the carbon metabolism and the cell cycle, were significantly enriched. The results provide fundamental evidence for the better understanding of lncRNAs' and differentially expressed genes' (DEGs) regulatory role in the molecular pathways governing milk production in pigeon crops. To our knowledge, this is the first genome-wide investigation of the lncRNAs in pigeon crop associated with milk production. This study provided valuable resources for differentially expressed lncRNAs and mRNAs, improving our understanding of the molecular mechanism of pigeon milk production.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jilan Chen
- Correspondence: ; Tel.: +86-10-6281-6005
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35
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Nordmann GC, Malkemper EP, Landler L, Ushakova L, Nimpf S, Heinen R, Schuechner S, Ogris E, Keays DA. A high sensitivity ZENK monoclonal antibody to map neuronal activity in Aves. Sci Rep 2020; 10:915. [PMID: 31969617 PMCID: PMC6976653 DOI: 10.1038/s41598-020-57757-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/20/2019] [Indexed: 01/04/2023] Open
Abstract
The transcription factor ZENK is an immediate early gene that has been employed as a surrogate marker to map neuronal activity in the brain. It has been used in a wide variety of species, however, commercially available antibodies have limited immunoreactivity in birds. To address this issue we generated a new mouse monoclonal antibody, 7B7-A3, raised against ZENK from the rock pigeon (Columba livia). We show that 7B7-A3 labels clZENK in both immunoblots and histological stainings with high sensitivity and selectivity for its target. Using a sound stimulation paradigm we demonstrate that 7B7-A3 can detect activity-dependent ZENK expression at key stations of the central auditory pathway of the pigeon. Finally, we compare staining efficiency across three avian species and confirm that 7B7-A3 is compatible with immunohistochemical detection of ZENK in the rock pigeon, zebra finch, and domestic chicken. Taken together, 7B7-A3 represents a useful tool for the avian neuroscience community to map functional activity in the brain.
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Affiliation(s)
- Gregory Charles Nordmann
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Erich Pascal Malkemper
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Lukas Landler
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Lyubov Ushakova
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Simon Nimpf
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Robert Heinen
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Stefan Schuechner
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Egon Ogris
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - David Anthony Keays
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
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36
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Nimpf S, Nordmann GC, Kagerbauer D, Malkemper EP, Landler L, Papadaki-Anastasopoulou A, Ushakova L, Wenninger-Weinzierl A, Novatchkova M, Vincent P, Lendl T, Colombini M, Mason MJ, Keays DA. A Putative Mechanism for Magnetoreception by Electromagnetic Induction in the Pigeon Inner Ear. Curr Biol 2019; 29:4052-4059.e4. [DOI: 10.1016/j.cub.2019.09.048] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022]
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37
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Í Kongsstovu S, Mikalsen SO, Homrum EÍ, Jacobsen JA, Flicek P, Dahl HA. Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly. Sci Rep 2019; 9:17716. [PMID: 31776409 PMCID: PMC6881392 DOI: 10.1038/s41598-019-54151-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and completeness of the assemblies. Results showed that the A2 assembly was less fragmented, more complete and more correct than A1. A3 showed improvement in fragmentation and correctness compared with A2 and the published assembly but was slightly less complete than the published assembly. Thus, we here confirmed the previously published herring assembly, and made improvements by further scaffolding the assembly and removing low-quality sequences using linked and long reads and merging of assemblies.
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Affiliation(s)
- Sunnvør Í Kongsstovu
- Amplexa Genetics A/S, Hoyvíksvegur 51, FO-100, Tórshavn, Faroe Islands. .,University of the Faroe Islands, Department of Science and Technology, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands. .,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Svein-Ole Mikalsen
- University of the Faroe Islands, Department of Science and Technology, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands
| | - Eydna Í Homrum
- Faroe Marine Research Institute, Nóatún 1, FO-100, Tórshavn, Faroe Islands
| | - Jan Arge Jacobsen
- Faroe Marine Research Institute, Nóatún 1, FO-100, Tórshavn, Faroe Islands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Hans Atli Dahl
- Amplexa Genetics A/S, Hoyvíksvegur 51, FO-100, Tórshavn, Faroe Islands
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38
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Dubinin MV, Belosludtsev KN. Taxonomic Features of Specific Ca2+ Transport Mechanisms in Mitochondria. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2019. [DOI: 10.1134/s1990747819030127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Jiang L, Bi D, Ding H, Ren Q, Wang P, Kan X. Identification and comparative profiling of gonadal microRNAs in the adult pigeon ( Columba livia). Br Poult Sci 2019; 60:638-648. [PMID: 31343256 DOI: 10.1080/00071668.2019.1639140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.
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Affiliation(s)
- L Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - D Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - H Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Q Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - P Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - X Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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40
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Pigeon foot feathering reveals conserved limb identity networks. Dev Biol 2019; 454:128-144. [PMID: 31247188 DOI: 10.1016/j.ydbio.2019.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022]
Abstract
The tetrapod limb is a stunning example of evolutionary diversity, with dramatic variation not only among distantly related species, but also between the serially homologous forelimbs (FLs) and hindlimbs (HLs) within species. Despite this variation, highly conserved genetic and developmental programs underlie limb development and identity in all tetrapods, raising the question of how limb diversification is generated from a conserved toolkit. In some breeds of domestic pigeon, shifts in the expression of two conserved limb identity transcription factors, PITX1 and TBX5, are associated with the formation of feathered HLs with partial FL identity. To determine how modulation of PITX1 and TBX5 expression affects downstream gene expression, we compared the transcriptomes of embryonic limb buds from pigeons with scaled and feathered HLs. We identified a set of differentially expressed genes enriched for genes encoding transcription factors, extracellular matrix proteins, and components of developmental signaling pathways with important roles in limb development. A subset of the genes that distinguish scaled and feathered HLs are also differentially expressed between FL and scaled HL buds in pigeons, pinpointing a set of gene expression changes downstream of PITX1 and TBX5 in the partial transformation from HL to FL identity. We extended our analyses by comparing pigeon limb bud transcriptomes to chicken, anole lizard, and mammalian datasets to identify deeply conserved PITX1- and TBX5-responsive components of the limb identity program. Our analyses reveal a suite of predominantly low-level gene expression changes that are conserved across amniotes to regulate the identity of morphologically distinct limbs.
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41
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Jones MEH, Button DJ, Barrett PM, Porro LB. Digital dissection of the head of the rock dove ( Columba livia) using contrast-enhanced computed tomography. ZOOLOGICAL LETTERS 2019; 5:17. [PMID: 31205748 PMCID: PMC6558907 DOI: 10.1186/s40851-019-0129-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
The rock dove (or common pigeon), Columba livia, is an important model organism in biological studies, including research focusing on head muscle anatomy, feeding kinematics, and cranial kinesis. However, no integrated computer-based biomechanical model of the pigeon head has yet been attempted. As an initial step towards achieving this goal, we present the first three-dimensional digital dissection of the pigeon head based on a contrast-enhanced computed tomographic dataset achieved using iodine potassium iodide as a staining agent. Our datasets enable us to visualize the skeletal and muscular anatomy, brain and cranial nerves, and major sense organs of the pigeon, including very small and fragile features, as well as maintaining the three-dimensional topology of anatomical structures. This work updates and supplements earlier anatomical work on this widely used laboratory organism. We resolve several key points of disagreement arising from previous descriptions of pigeon anatomy, including the precise arrangement of the external adductor muscles and their relationship to the posterior adductor. Examination of the eye muscles highlights differences between avian taxa and shows that pigeon eye muscles are more similar to those of a tinamou than they are to those of a house sparrow. Furthermore, we present our three-dimensional data as publicly accessible files for further research and education purposes. Digital dissection permits exceptional visualisation and will be a valuable resource for further investigations into the head anatomy of other bird species, as well as efforts to reconstruct soft tissues in fossil archosaurs.
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Affiliation(s)
- Marc E. H. Jones
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD UK
| | - David J. Button
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD UK
| | - Paul M. Barrett
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD UK
| | - Laura B. Porro
- Department of Cell and Developmental Biology, UCL, University College London, Gower Street, London, WC1E 6BT UK
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42
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Domyan ET, Hardy J, Wright T, Frazer C, Daniels J, Kirkpatrick J, Kirkpatrick J, Wakamatsu K, Hill JT. SOX10 regulates multiple genes to direct eumelanin versus pheomelanin production in domestic rock pigeon. Pigment Cell Melanoma Res 2019; 32:634-642. [PMID: 30838786 PMCID: PMC6850303 DOI: 10.1111/pcmr.12778] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 02/16/2019] [Accepted: 02/25/2019] [Indexed: 12/24/2022]
Abstract
The domesticated rock pigeon (Columba livia) has been bred for hundreds of years to display an immense variety of ornamental attributes such as feather color and color patterns. Color is influenced by multiple loci that impact the type and amount of melanin deposited on the feathers. Pigeons homozygous for the "recessive red" mutation, which causes downregulation of Sox10, display brilliant red feathers instead of blue/black feathers. Sox10 encodes a transcription factor important for melanocyte differentiation and function, but the genes that mediate its promotion of black versus red pigment are unknown. Here, we present a transcriptomic comparison of regenerating feathers from wild-type and recessive red pigeons to identify candidate SOX10 targets. Our results identify both known and novel targets, including many genes not previously implicated in pigmentation. These data highlight the value of using novel, emerging model organisms to gain insight into the genetic basis of pigment variation.
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Affiliation(s)
- Eric T Domyan
- Department of Biology, Utah Valley University, Orem, Utah
| | - Jeremy Hardy
- Department of Biology, Utah Valley University, Orem, Utah
| | - Tanner Wright
- Department of Biology, Utah Valley University, Orem, Utah
| | - Cody Frazer
- Department of Biology, Utah Valley University, Orem, Utah
| | - Jordan Daniels
- Department of Biology, Utah Valley University, Orem, Utah
| | | | | | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Jonathon T Hill
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah
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43
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Ruvinskiy D, Larkin DM, Farré M. A Near Chromosome Assembly of the Dromedary Camel Genome. Front Genet 2019; 10:32. [PMID: 30804979 PMCID: PMC6371769 DOI: 10.3389/fgene.2019.00032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 01/11/2023] Open
Abstract
The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of milk and meat. Much like cattle and horses, the camel may be found in industrial farming conditions as well as used in sporting. Camel racing is a multi-million dollar industry, with some specimens being valued at upward of 9.5 million USD. Despite its apparent value to humans, the dromedary camel is a neglected species in genomics. While cattle and other domesticated species have had much attention in terms of genome assembly, the camel has only been assembled to scaffold level, which does not give a clear indication of the order or chromosomal location of sequenced fragments. In this study, the Reference Assistant Chromosome Assembly (RACA) algorithm was implemented to use read-pair information of camel scaffolds, aligned with the cattle and human genomes in order to organize and orient these scaffolds in a near-chromosome level assembly. This method generated 72 large size fragments (N50 54.36 Mb). These predicted chromosome fragments (PCFs) were then compared with comparative maps of camel and cytogenetic map of alpaca chromosomes, allowing us to further upgrade the assembly. This dromedary camel assembly will be an invaluable tool to verify future camel assemblies generated with chromatin conformation or/and long read technologies. This study provides the first near-chromosome assembly of the dromedary camel, thus adding this economically important species to a growing pool of knowledge regarding the genome structure of domesticated livestock.
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Affiliation(s)
- Daniil Ruvinskiy
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom
| | - Denis M Larkin
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.,The Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marta Farré
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.,School of Biosciences, University of Kent, Canterbury, United Kingdom
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44
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Abstract
Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results.
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Affiliation(s)
- Mathieu Seppey
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland
| | - Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland.
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45
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Ng CS, Li WH. Genetic and Molecular Basis of Feather Diversity in Birds. Genome Biol Evol 2018; 10:2572-2586. [PMID: 30169786 PMCID: PMC6171735 DOI: 10.1093/gbe/evy180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 12/16/2022] Open
Abstract
Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago
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46
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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47
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Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 2018; 7:e34803. [PMID: 30014848 PMCID: PMC6050045 DOI: 10.7554/elife.34803] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
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Affiliation(s)
- Anna I Vickrey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Rebecca Bruders
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Zev Kronenberg
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Emma Mackey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Emily T Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Raquel Maynez
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Edward J Osborne
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana-ChampaignChampaignUnited States
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Mark Yandell
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Michael D Shapiro
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
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