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Zhang L, Bai L, Wang J, Wan D, Liang W. Occupation rates of artificial nest boxes by secondary cavity-nesting birds: The influence of nest site characteristics. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Jiang H, Lin JQ, Sun L, Xu YC, Fang SG. Sex-Biased Gene Expression and Evolution in the Cerebrum and Syrinx of Chinese Hwamei ( Garrulax canorus). Genes (Basel) 2021; 12:genes12040569. [PMID: 33919806 PMCID: PMC8070764 DOI: 10.3390/genes12040569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
It is common that males and females display sexual dimorphisms, which usually result from sex-biased gene expression. Chinese hwamei (Garrulax canorus) is a good model for studying sex-biased gene expression because the song between the sexes is quite different. In this study, we analyze cerebrum and syrinx sex-biased gene expression and evolution using the de novo assembled Chinese hwamei transcriptome. In both the cerebrum and syrinx, our study revealed that most female-biased genes were actively expressed in females only, while most male-biased genes were actively expressed in both sexes. In addition, both male- and female-biased genes were enriched on the putative Z chromosome, suggesting the existence of sexually antagonistic genes and the insufficient dosage compensation of the Z-linked genes. We also identified a 9 Mb sex linkage region on the putative 4A chromosome which enriched more than 20% of female-biased genes. Resultantly, male-biased genes in both tissues had significantly higher Ka/Ks and effective number of codons (ENCs) than unbiased genes, and this suggested that male-biased genes which exhibit accelerated divergence may have resulted from positive selection. Taken together, our results initially revealed the reasons for the differences in singing behavior between males and females of Chinese hwamei.
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Affiliation(s)
- Hua Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Li Sun
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Yan-Chun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China;
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation, Harbin 150040, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
- Correspondence: ; Tel.: +86-571-88206472
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3
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Xu L, Irestedt M, Zhou Q. Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds. Genes (Basel) 2020; 11:E1267. [PMID: 33126459 PMCID: PMC7692361 DOI: 10.3390/genes11111267] [Citation(s) in RCA: 4] [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: 09/23/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin's finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.
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Affiliation(s)
- Luohao Xu
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden;
| | - Qi Zhou
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310012, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310012, China
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4
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Botero-Delgadillo E, Gilsenan C, Mueller JC, Kempenaers B. Negative effects of individual heterozygosity on reproductive success in a wild bird population. Mol Ecol 2020; 29:3196-3216. [PMID: 32668071 DOI: 10.1111/mec.15553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023]
Abstract
The evolutionary consequences of individual genetic diversity are frequently studied by assessing heterozygosity-fitness correlations (HFCs). The prevalence of positive and negative HFCs and the predominance of general versus local effects in wild populations are far from understood, partly because comprehensive studies testing for both inbreeding and outbreeding depression are lacking. We studied a genetically diverse population of blue tits in southern Germany using a genome-wide set of 87 microsatellites to investigate the relationship between proxies of reproductive success and measures of multilocus and single-locus individual heterozygosity (MLH and SLH). We used complimentary measures of MLH and partitioned markers into functional categories according to their position in the blue tit genome. HFCs based on MLH were consistently negative for functional loci, whereas correlations were rather inconsistent for loci found in nonfunctional areas of the genome. Clutch size was the only reproductive variable showing a general effect. We found evidence for local effects for three measures of reproductive success: arrival date at the breeding site, the probability of breeding at the study site and male reproductive success. For these, we observed consistent, and relatively strong, negative effects at one functional locus. Remarkably, this marker had a similar effect in another blue tit population from Austria (~400 km to the east). We suggest that a genetic local effect on timing of arrival might be responsible for most negative HFCs detected, with carry-over effects on other reproductive traits. This effect could reflect individual differences in the distance between overwintering areas and breeding sites.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Carol Gilsenan
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
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5
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Sun D, Maney DL, Layman TS, Chatterjee P, Yi SV. Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system. Genome Res 2019; 29:1673-1684. [PMID: 31548356 PMCID: PMC6771406 DOI: 10.1101/gr.248641.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 08/07/2019] [Indexed: 01/26/2023]
Abstract
In male heterogametic systems, the X Chromosome is epigenetically differentiated between males and females, to facilitate dosage compensation. For example, the X Chromosome in female mammals is largely inactivated. Relative to well-studied male heterogametic systems, the extent of epigenetic differentiation between male and female Z Chromosomes in female heterogametic species, which often lack complete dosage compensation, is poorly understood. Here, we examined the chromosomal DNA methylation landscapes of male and female Z Chromosomes in two distantly related avian species, namely chicken and white-throated sparrow. We show that, in contrast to the pattern in mammals, male and female Z Chromosomes in these species exhibit highly similar patterns of DNA methylation, which is consistent with weak or absent dosage compensation. We further demonstrate that the epigenetic differences between male and female chicken Z Chromosomes are localized to a few regions, including a previously identified male hypermethylated region 1 (MHM1; CGNC: 80601). We discovered a novel region with elevated male-to-female methylation ratios on the chicken Z Chromosome (male hypermethylated region 2 [MHM2]; CGNC: 80602). The MHM1 and MHM2, despite little sequence similarity between them, bear similar molecular features that are likely associated with their functions. We present evidence consistent with female hypomethylation of MHMs and up-regulation of nearby genes. Therefore, despite little methylation differentiation between sexes, extremely localized DNA methylation differences between male and female chicken Z Chromosomes have evolved and affect expression of nearby regions. Our findings offer new insights into epigenetic regulation of gene expression between sexes in female heterogametic systems.
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Affiliation(s)
- Dan Sun
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, Georgia 30322, USA
| | - Thomas S Layman
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Paramita Chatterjee
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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6
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Cossard GG, Toups MA, Pannell JR. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. ANNALS OF BOTANY 2019; 123:1119-1131. [PMID: 30289430 PMCID: PMC6612945 DOI: 10.1093/aob/mcy183] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/06/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species. METHODS The present study documents differences in gene expression in both above- and below-ground tissues of early pre-reproductive individuals of the wind-pollinated dioecious annual herb, Mercurialis annua, which otherwise shows clear sexual dimorphism only at the adult stage. KEY RESULTS Whereas males and females differed in their gene expression at the first leaf stage, sex-biased gene expression peaked just prior to, and after, flowering, as might be expected if sexual dimorphism is partly a response to differential costs of reproduction. Sex-biased genes were over-represented among putative sex-linked genes in M. annua but showed no evidence for more rapid evolution than unbiased genes. CONCLUSIONS Sex-biased gene expression in M. annua occurs as early as the first whorl of leaves is produced, is highly dynamic during plant development and varies substantially between vegetative tissues.
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Affiliation(s)
- Guillaume G Cossard
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Melissa A Toups
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - John R Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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7
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Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Curr Biol 2019; 29:1712-1720.e7. [PMID: 31080084 PMCID: PMC6538971 DOI: 10.1016/j.cub.2019.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/16/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.
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Affiliation(s)
- Toni I Gossmann
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK; Bielefeld University, Department of Animal Behaviour, 33501 Bielefeld, Germany
| | - Achchuthan Shanmugasundram
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Ludovic Duvaux
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France; BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Lemaire
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany; Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Lee D Roberts
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Sophia Schade
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Johanna M Gostner
- Division of Medical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Falk Hildebrand
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Enrica Calvani
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm 171 65, Sweden
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Dominique Allaine
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - Aurélie Cohas
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany.
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8
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Kolchanova S, Kliver S, Komissarov A, Dobrinin P, Tamazian G, Grigorev K, Wolfsberger WW, Majeske AJ, Velez-Valentin J, Valentin de la Rosa R, Paul-Murphy JR, Guzman DSM, Court MH, Rodriguez-Flores JL, Martínez-Cruzado JC, Oleksyk TK. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes (Basel) 2019; 10:E54. [PMID: 30654561 PMCID: PMC6356210 DOI: 10.3390/genes10010054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/13/2018] [Accepted: 01/08/2019] [Indexed: 11/17/2022] Open
Abstract
Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.
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Affiliation(s)
- Sofiia Kolchanova
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany.
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Aleksei Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Pavel Dobrinin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Kirill Grigorev
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
| | - Walter W Wolfsberger
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biological Sciences, Oakland University, 118 Library Drive, Rochester, MI 48309, USA.
- Department of Biological Sciences, Uzhhorod National University, 88000 Uzhhorod, Ukraine.
| | - Audrey J Majeske
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Beaumont BioBank, William Beaumont Hospital, Royal Oak, MI 48073, USA.
| | - Jafet Velez-Valentin
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande, PR 00745, USA.
| | - Ricardo Valentin de la Rosa
- The Recovery Program of the Puerto Rican Parrot at the Rio Abajo State Forest, Departamento de Recursos Naturales y Ambientales de Puerto Rico, Arecibo, PR 00613, USA.
| | - Joanne R Paul-Murphy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - David Sanchez-Migallon Guzman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - Michael H Court
- Program in Individualized Medicine (PrIMe), Pharmacogenomics Laboratory, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, 100 Grimes Way, Pullman, WA 99164, USA.
| | | | | | - Taras K Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biological Sciences, Oakland University, 118 Library Drive, Rochester, MI 48309, USA.
- Department of Biological Sciences, Uzhhorod National University, 88000 Uzhhorod, Ukraine.
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9
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Valcu CM, Scheltema RA, Schweiggert RM, Valcu M, Teltscher K, Walther DM, Carle R, Kempenaers B. Life history shapes variation in egg composition in the blue tit Cyanistes caeruleus. Commun Biol 2019; 2:6. [PMID: 30740542 PMCID: PMC6320336 DOI: 10.1038/s42003-018-0247-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/02/2018] [Indexed: 12/26/2022] Open
Abstract
Maternal investment directly shapes early developmental conditions and therefore has long-term fitness consequences for the offspring. In oviparous species prenatal maternal investment is fixed at the time of laying. To ensure the best survival chances for most of their offspring, females must equip their eggs with the resources required to perform well under various circumstances, yet the actual mechanisms remain unknown. Here we describe the blue tit egg albumen and yolk proteomes and evaluate their potential to mediate maternal effects. We show that variation in egg composition (proteins, lipids, carotenoids) primarily depends on laying order and female age. Egg proteomic profiles are mainly driven by laying order, and investment in the egg proteome is functionally biased among eggs. Our results suggest that maternal effects on egg composition result from both passive and active (partly compensatory) mechanisms, and that variation in egg composition creates diverse biochemical environments for embryonic development.
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Affiliation(s)
- Cristina-Maria Valcu
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Richard A. Scheltema
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Ralf M. Schweiggert
- Plant Foodstuff Technology and Analysis, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Mihai Valcu
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Kim Teltscher
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Dirk M. Walther
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Reinhold Carle
- Plant Foodstuff Technology and Analysis, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
- Biological Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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10
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Catalán A, Macias-Muñoz A, Briscoe AD. Evolution of Sex-Biased Gene Expression and Dosage Compensation in the Eye and Brain of Heliconius Butterflies. Mol Biol Evol 2018; 35:2120-2134. [DOI: 10.1093/molbev/msy111] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ana Catalán
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians Universität, Planegg-Martinsried, Germany
| | - Aide Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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11
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Gschloessl B, Dorkeld F, Berges H, Beydon G, Bouchez O, Branco M, Bretaudeau A, Burban C, Dubois E, Gauthier P, Lhuillier E, Nichols J, Nidelet S, Rocha S, Sauné L, Streiff R, Gautier M, Kerdelhué C. Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Mol Ecol Resour 2018; 18:602-619. [PMID: 29352511 DOI: 10.1111/1755-0998.12756] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 12/23/2017] [Accepted: 01/03/2018] [Indexed: 12/15/2022]
Abstract
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).
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Affiliation(s)
- B Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - F Dorkeld
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - H Berges
- INRA-CNRGV, Castanet Tolosan Cedex, France
| | - G Beydon
- INRA-CNRGV, Castanet Tolosan Cedex, France
| | - O Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan Cedex, France
| | - M Branco
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), University of Lisbon (ULisboa), Lisboa, Portugal
| | - A Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Rennes, France
| | - C Burban
- BIOGECO, INRA, Univ. Bordeaux, Cestas, France
| | - E Dubois
- Plateforme MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle IGF-sud, UMR 5203 CNRS-U 661 INSERM-Université de Montpellier, Montpellier Cedex 05, France
| | - P Gauthier
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - E Lhuillier
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan Cedex, France
| | - J Nichols
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, UK
| | - S Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.,Plateforme MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle IGF-sud, UMR 5203 CNRS-U 661 INSERM-Université de Montpellier, Montpellier Cedex 05, France
| | - S Rocha
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), University of Lisbon (ULisboa), Lisboa, Portugal
| | - L Sauné
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - R Streiff
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - M Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - C Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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12
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Koglin S, Trense D, Wink M, Sauer-Gürth H, Tietze DT. Characterization of a de novo assembled transcriptome of the Common Blackbird ( Turdus merula). PeerJ 2017; 5:e4045. [PMID: 29255646 PMCID: PMC5732540 DOI: 10.7717/peerj.4045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. METHODS Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. RESULTS Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. DISCUSSION Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.
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Affiliation(s)
- Sven Koglin
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Daronja Trense
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Michael Wink
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Hedwig Sauer-Gürth
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Dieter Thomas Tietze
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
- Current affiliation: Natural History Museum Basel, Basel, Switzerland
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13
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Tigano A, Sackton TB, Friesen VL. Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia). Mol Ecol Resour 2017; 18:79-90. [PMID: 28815912 DOI: 10.1111/1755-0998.12712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Abstract
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray/sscape, soapdenovo2 and platanus, in assembling the highly heterozygous genome of the thick-billed murre. Our results show that platanus, an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick-billed murre genome using a homology-based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.
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Affiliation(s)
- Anna Tigano
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Vicki L Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
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Capilla-Lasheras P, Dominoni DM, Babayan SA, O'Shaughnessy PJ, Mladenova M, Woodford L, Pollock CJ, Barr T, Baldini F, Helm B. Elevated Immune Gene Expression Is Associated with Poor Reproductive Success of Urban Blue Tits. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00064] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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15
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Narum S, Chambers K. Editorial 2017. Mol Ecol Resour 2017; 17:129-137. [DOI: 10.1111/1755-0998.12651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Gautier M, Klassmann A, Vitalis R. rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Mol Ecol Resour 2016; 17:78-90. [PMID: 27863062 DOI: 10.1111/1755-0998.12634] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/29/2016] [Accepted: 10/31/2016] [Indexed: 01/01/2023]
Abstract
Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g. EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. The rehh package for r was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance was not sufficient to cope with the growing size of available data sets. Here, we propose a major upgrade of the rehh package, which includes an improved processing of the input files, a faster algorithm to enumerate haplotypes, as well as multithreading. As illustrated with the analysis of large human haplotype data sets, these improvements decrease the computation time by more than one order of magnitude. This new version of rehh will thus allow performing iHS-, Rsb- or XP-EHH-based scans on large data sets. The package rehh 2.0 is available from the CRAN repository (http://cran.r-project.org/web/packages/rehh/index.html) together with help files and a detailed manual.
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Affiliation(s)
- Mathieu Gautier
- INRA, UMR CBGP, Montferrier-sur-Lez, F-34988, France.,Institut de Biologie Computationnelle, Montpellier, F-34095, France
| | | | - Renaud Vitalis
- INRA, UMR CBGP, Montferrier-sur-Lez, F-34988, France.,Institut de Biologie Computationnelle, Montpellier, F-34095, France
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17
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Santure AW. An ecological model organism flies into the genomics era. Mol Ecol Resour 2016; 16:379-81. [PMID: 26813493 DOI: 10.1111/1755-0998.12491] [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: 11/03/2015] [Accepted: 11/13/2015] [Indexed: 11/26/2022]
Abstract
Despite the very rapid 'genomicization' of the field of Molecular Ecology in recent years, there have been relatively few annotated whole-genome assemblies of nonmodel organisms published. Instead, molecular ecologists have more frequently utilized next-generation sequencing technologies to develop genome-wide markers or to generate transcriptome data. Whole-genome assemblies are more expensive and require considerable computational resources and bioinformatic expertise. However, the availability of an annotated genome offers exciting opportunities to address fundamental questions in ecology and evolution that are difficult to address with moderate sets of markers or by transcriptome sequencing. Such questions include elucidating the roles of natural and sexual selection in shaping diversity, determining the roles of regulatory and protein-coding change in the evolution of traits, and determining the genomic architecture of sex-specific trait variation. Arguably, these questions are most tractable--and most interesting--in well-characterized species for which there is already some knowledge of natural and sexual selection, and of the traits that are most likely to link to fitness. In this issue, Mueller et al. (2016) present the assembly and annotation of the genome of the blue tit (Cyanistes caeruleus), a model ecological species. In addition, by sequencing the transcriptome of male and female blue tits, the authors identify and annotate sex-biased gene expression and conclude that noncoding RNA genes are likely to play a significant role in sex-biased expression. By making their assembly and annotation publically available and accessible via a genome browser, Mueller et al. (2016) offer exciting possibilities for further research into the genomic basis of adaptation, and investigation of the roles of natural and sexual selection, in this well-studied ecological model species.
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Affiliation(s)
- Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
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Abstract
The recent availability of multiple avian genomes has laid the foundation for a huge variety of comparative genomics analyses including scans for changes and signatures of selection that arose from adaptions to new ecological niches. Nocturnal adaptation in birds, unlike in mammals, is comparatively recent, a fact that makes birds good candidates for identifying early genetic changes that support adaptation to dim-light environments. In this review, we give examples of comparative genomics analyses that could shed light on mechanisms of adaptation to nocturnality. We present advantages and disadvantages of both "data-driven" and "hypothesis-driven" approaches that lead to the discovery of candidate genes and genetic changes promoting nocturnality. We anticipate that the accessibility of multiple genomes from the Genome 10K Project will allow a better understanding of evolutionary mechanisms and adaptation in general.
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Affiliation(s)
- Diana Le Duc
- Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Torsten Schöneberg
- Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Leipzig, Germany
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