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Sachslehner AP, Surbek M, Holthaus KB, Steinbinder J, Golabi B, Hess C, Eckhart L. The Evolution of Transglutaminases Underlies the Origin and Loss of Cornified Skin Appendages in Vertebrates. Mol Biol Evol 2024; 41:msae100. [PMID: 38781495 DOI: 10.1093/molbev/msae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/11/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Transglutaminases (TGMs) cross-link proteins by introducing covalent bonds between glutamine and lysine residues. These cross-links are essential for epithelial cornification which enables tetrapods to live on land. Here, we investigated which evolutionary adaptations of vertebrates were associated with specific changes in the family of TGM genes. We determined the catalog of TGMs in the main clades of vertebrates, performed a comprehensive phylogenetic analysis of TGMs, and localized the distribution of selected TGMs in tissues. Our data suggest that TGM1 is the phylogenetically oldest epithelial TGM, with orthologs being expressed in the cornified teeth of the lamprey, a basal vertebrate. Gene duplications led to the origin of TGM10 in stem vertebrates, the origin of TGM2 in jawed vertebrates, and an increasing number of epithelium-associated TGM genes in the lineage leading to terrestrial vertebrates. TGM9 is expressed in the epithelial egg tooth, and its evolutionary origin in stem amniotes coincided with the evolution of embryonic development in eggs that are surrounded by a protective shell. Conversely, viviparous mammals have lost both the epithelial egg tooth and TGM9. TGM3 and TGM6 evolved as regulators of cornification in hair follicles and underwent pseudogenization upon the evolutionary loss of hair in cetaceans. Taken together, this study reveals the gain and loss of vertebrate TGM genes in association with the evolution of cornified skin appendages and suggests an important role of TGM9 in the evolution of amniotes.
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Affiliation(s)
| | - Marta Surbek
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
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Arai E, Hasegawa M, Wakamatsu K, Ito S. Males with More Pheomelanin Have a Lower Oxidative Balance in Asian Barn Swallows (Hirundo rustica gutturalis). Zoolog Sci 2018; 35:505-513. [DOI: 10.2108/zs170204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Emi Arai
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0115, Japan
| | - Masaru Hasegawa
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0115, Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi 470-1192, Japan
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi 470-1192, Japan
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Wang L, Yu C, Guo L, Lin H, Meng Z. In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus). PLoS One 2015; 10:e0145868. [PMID: 26713756 PMCID: PMC4700983 DOI: 10.1371/journal.pone.0145868] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/09/2015] [Indexed: 11/28/2022] Open
Abstract
The common coral trout is one species of major importance in commercial fisheries and aquaculture. Recently, two different color morphs of Plectropomus leopardus were discovered and the biological importance of the color difference is unknown. Since coral trout species are poorly characterized at the molecular level, we undertook the transcriptomic characterization of the two color morphs, one black and one red coral trout, using Illumina next generation sequencing technologies. The study produced 55162966 and 54588952 paired-end reads, for black and red trout, respectively. De novo transcriptome assembly generated 95367 and 99424 unique sequences in black and red trout, respectively, with 88813 sequences shared between them. Approximately 50% of both trancriptomes were functionally annotated by BLAST searches against protein databases. The two trancriptomes were enriched into 25 functional categories and showed similar profiles of Gene Ontology category compositions. 34110 unigenes were grouped into 259 KEGG pathways. Moreover, we identified 14649 simple sequence repeats (SSRs) and designed primers for potential application. We also discovered 130524 putative single nucleotide polymorphisms (SNPs) in the two transcriptomes, supplying potential genomic resources for the coral trout species. In addition, we identified 936 fast-evolving genes and 165 candidate genes under positive selection between the two color morphs. Finally, 38 candidate genes underlying the mechanism of color and pigmentation were also isolated. This study presents the first transcriptome resources for the common coral trout and provides basic information for the development of genomic tools for the identification, conservation, and understanding of the speciation and local adaptation of coral reef fish species.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cuiping Yu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liang Guo
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- * E-mail:
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López-Arrabé J, Cantarero A, Pérez-Rodríguez L, Palma A, Moreno J. Plumage ornaments and reproductive investment in relation to oxidative status in the Iberian Pied Flycatcher (Ficedula hypoleuca iberiae). CAN J ZOOL 2014. [DOI: 10.1139/cjz-2014-0199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A key aspect in the study of plumage traits with a potential role in communication is the cost associated with trait production and maintenance, expressed in terms of oxidative stress. In the Iberian Pied Flycatcher (Ficedula hypoleuca iberiae (Witherby, 1928)), males and some females exhibit a white forehead patch and both sexes present conspicuous white patches on the wings. We examined associations between these plumage ornaments and their ability to cope with oxidative stress. Furthermore, we explored oxidative costs of reproductive investment. Total antioxidant status (TAS) in plasma and glutathione (tGSH) levels in red blood cells, as well as a marker of oxidative damage in plasma lipids (malondialdehyde (MDA)), were assessed simultaneously for the first time in studies of avian reproduction. We found negative associations between antioxidants and ornaments in incubating females, although this relationship was positive while feeding nestlings. For males, MDA levels were negatively associated with ornaments, while TAS showed a positive relation. Female MDA showed a positive correlation with intensity of incubation attendance, while this relation was negative for tGSH levels. These results indicate that multiple achromatic plumage ornaments signal the individual capacity to cope with costs related to oxidative stress. Moreover, this study highlights the critical role of incubation for avian life histories.
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Affiliation(s)
- Jimena López-Arrabé
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Departamento de Ecología Evolutiva, Calle de José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Alejandro Cantarero
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Departamento de Ecología Evolutiva, Calle de José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Lorenzo Pérez-Rodríguez
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Departamento de Ecología Evolutiva, Avenida Américo Vespucio s/n, Isla de la Cartuja, 41092 Sevilla, Spain
| | - Antonio Palma
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Departamento de Ecología Evolutiva, Calle de José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Departamento de Ecología Evolutiva, Calle de José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Sun K, Meiklejohn KA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc Biol Sci 2014; 281:20140823. [PMID: 25030982 PMCID: PMC4123699 DOI: 10.1098/rspb.2014.0823] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/24/2014] [Indexed: 11/12/2022] Open
Abstract
The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibit substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation.
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Affiliation(s)
- Keping Sun
- Department of Biology, University of Florida, Gainesville, FL, USA Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | | | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
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Kawakami T, Smeds L, Backström N, Husby A, Qvarnström A, Mugal CF, Olason P, Ellegren H. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Mol Ecol 2014; 23:4035-58. [PMID: 24863701 PMCID: PMC4149781 DOI: 10.1111/mec.12810] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 12/15/2022]
Abstract
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
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Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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Emaresi G, Ducrest AL, Bize P, Richter H, Simon C, Roulin A. Pleiotropy in the melanocortin system: expression levels of this system are associated with melanogenesis and pigmentation in the tawny owl (Strix aluco). Mol Ecol 2013; 22:4915-30. [PMID: 24033481 DOI: 10.1111/mec.12438] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 01/22/2023]
Abstract
The adaptive function of melanin-based coloration is a long-standing debate. A recent genetic model suggested that pleiotropy could account for covariations between pigmentation, behaviour, morphology, physiology and life history traits. We explored whether the expression levels of genes belonging to the melanocortin system (MC1R, POMC, PC1/3, PC2 and the antagonist ASIP), which have many pleiotropic effects, are associated with melanogenesis (through variation in the expression of the genes MITF, SLC7A11, TYR, TYRP1) and in turn melanin-based coloration. We considered the tawny owl (Strix aluco) because individuals vary continuously from light to dark reddish, and thus, colour variation is likely to stem from differences in the levels of gene expression. We measured gene expression in feather bases collected in nestlings at the time of melanin production. As expected, the melanocortin system was associated with the expression of melanogenic genes and pigmentation. Offspring of darker reddish fathers expressed PC1/3 to lower levels but tended to express PC2 to higher levels. The convertase enzyme PC1/3 cleaves the POMC prohormone to obtain ACTH, while the convertase enzyme PC2 cleaves ACTH to produce α-melanin-stimulating hormone (α-MSH). ACTH regulates glucocorticoids, hormones that modulate stress responses, while α-MSH induces eumelanogenesis. We therefore conclude that the melanocortin system, through the convertase enzymes PC1/3 and PC2, may account for part of the interindividual variation in melanin-based coloration in nestling tawny owls. Pleiotropy may thus account for the covariation between phenotypic traits involved in social interactions (here pigmentation) and life history, morphology, behaviour and physiology.
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Affiliation(s)
- Guillaume Emaresi
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
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Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA. Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Mol Ecol 2013; 22:3216-41. [DOI: 10.1111/mec.12309] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 02/01/2023]
Affiliation(s)
- C. R. Primmer
- Department of Biology; University of Turku; 20014 Turku Finland
| | - S. Papakostas
- Department of Biology; University of Turku; 20014 Turku Finland
| | - E. H. Leder
- Department of Biology; University of Turku; 20014 Turku Finland
| | - M. J. Davis
- Institute for Molecular Bioscience; The University of Queensland; Brisbane Qld 4072 Australia
| | - M. A. Ragan
- Institute for Molecular Bioscience; The University of Queensland; Brisbane Qld 4072 Australia
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Roulin A, Ducrest AL. Genetics of colouration in birds. Semin Cell Dev Biol 2013; 24:594-608. [PMID: 23665152 DOI: 10.1016/j.semcdb.2013.05.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 04/19/2013] [Accepted: 05/01/2013] [Indexed: 01/01/2023]
Abstract
Establishing the links between phenotype and genotype is of great importance for resolving key questions about the evolution, maintenance and adaptive function of phenotypic variation. Bird colouration is one of the most studied systems to investigate the role of natural and sexual selection in the evolution of phenotypic diversity. Given the recent advances in molecular tools that allow discovering genetic polymorphisms and measuring gene and protein expression levels, it is timely to review the literature on the genetics of bird colouration. The present study shows that melanin-based colour phenotypes are often associated with mutations at melanogenic genes. Differences in melanin-based colouration are caused by switches of eumelanin to pheomelanin production or by changes in feather keratin structure, melanoblast migration and differentiation, as well as melanosome structure. Similar associations with other types of colourations are difficult to establish, because our knowledge about the molecular genetics of carotenoid-based and structural colouration is quasi inexistent. This discrepancy stems from the fact that only melanin-based colouration shows pronounced heritability estimates, i.e. the resemblance between related individuals is usually mainly explained by genetic factors. In contrast, the expression of carotenoid-based colouration is phenotypically plastic with a high sensitivity to variation in environmental conditions. It therefore appears that melanin-based colour traits are prime systems to understand the genetic basis of phenotypic variation. In this context, birds have a great potential to bring us to new frontiers where many exciting discoveries will be made on the genetics of phenotypic traits, such as colouration. In this context, a major goal of our review is to suggest a number of exciting future avenues.
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Affiliation(s)
- Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Wolf JBW. Principles of transcriptome analysis and gene expression quantification: an
RNA
‐seq tutorial. Mol Ecol Resour 2013; 13:559-72. [DOI: 10.1111/1755-0998.12109] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 01/03/2023]
Affiliation(s)
- Jochen B. W. Wolf
- Department of Evolutionary Biology Uppsala University Uppsala Sweden
- Science of Life Laboratory Uppsala Sweden
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