151
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Twyman H, Valenzuela N, Literman R, Andersson S, Mundy NI. Seeing red to being red: conserved genetic mechanism for red cone oil droplets and co-option for red coloration in birds and turtles. Proc Biol Sci 2017; 283:rspb.2016.1208. [PMID: 27488652 DOI: 10.1098/rspb.2016.1208] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/14/2016] [Indexed: 11/12/2022] Open
Abstract
Avian ketocarotenoid pigments occur in both the red retinal oil droplets that contribute to colour vision and bright red coloration used in signalling. Turtles are the only other tetrapods with red retinal oil droplets, and some also display red carotenoid-based coloration. Recently, the CYP2J19 gene was strongly implicated in ketocarotenoid synthesis in birds. Here, we investigate CYP2J19 evolution in relation to colour vision and red coloration in reptiles using genomic and expression data. We show that turtles, but not crocodiles or lepidosaurs, possess a CYP2J19 orthologue, which arose via gene duplication before turtles and archosaurs split, and which is strongly and specifically expressed in the ketocarotenoid-containing retina and red integument. We infer that CYP2J19 initially functioned in colour vision in archelosaurs and conclude that red ketocarotenoid-based coloration evolved independently in birds and turtles via gene regulatory changes of CYP2J19 Our results suggest that red oil droplets contributed to colour vision in dinosaurs and pterosaurs.
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Affiliation(s)
- Hanlu Twyman
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011, USA
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011, USA
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg 40530, Sweden
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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152
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Putative Independent Evolutionary Reversals from Genotypic to Temperature-Dependent Sex Determination are Associated with Accelerated Evolution of Sex-Determining Genes in Turtles. J Mol Evol 2017; 86:11-26. [DOI: 10.1007/s00239-017-9820-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/18/2017] [Indexed: 12/14/2022]
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153
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Marin R, Cortez D, Lamanna F, Pradeepa MM, Leushkin E, Julien P, Liechti A, Halbert J, Brüning T, Mössinger K, Trefzer T, Conrad C, Kerver HN, Wade J, Tschopp P, Kaessmann H. Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage. Genome Res 2017; 27:1974-1987. [PMID: 29133310 PMCID: PMC5741051 DOI: 10.1101/gr.223727.117] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Abstract
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.
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Affiliation(s)
- Ray Marin
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Diego Cortez
- Center for Genomic Sciences, UNAM, CP62210 Cuernavaca, Mexico
| | - Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Madapura M Pradeepa
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Philippe Julien
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Katharina Mössinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Timo Trefzer
- Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany
| | - Christian Conrad
- Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany
| | - Halie N Kerver
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Juli Wade
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA.,Department of Psychology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Patrick Tschopp
- Institute of Zoology, University of Basel, 4051 Basel, Switzerland
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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154
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Desfilis E, Abellán A, Sentandreu V, Medina L. Expression of regulatory genes in the embryonic brain of a lizard and implications for understanding pallial organization and evolution. J Comp Neurol 2017; 526:166-202. [PMID: 28891227 PMCID: PMC5765483 DOI: 10.1002/cne.24329] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/13/2017] [Accepted: 09/01/2017] [Indexed: 02/03/2023]
Abstract
The comparison of gene expression patterns in the embryonic brain of mouse and chicken is being essential for understanding pallial organization. However, the scarcity of gene expression data in reptiles, crucial for understanding evolution, makes it difficult to identify homologues of pallial divisions in different amniotes. We cloned and analyzed the expression of the genes Emx1, Lhx2, Lhx9, and Tbr1 in the embryonic telencephalon of the lacertid lizard Psammodromus algirus. The comparative expression patterns of these genes, critical for pallial development, are better understood when using a recently proposed six‐part model of pallial divisions. The lizard medial pallium, expressing all genes, includes the medial and dorsomedial cortices, and the majority of the dorsal cortex, except the region of the lateral cortical superposition. The latter is rich in Lhx9 expression, being excluded as a candidate of dorsal or lateral pallia, and may belong to a distinct dorsolateral pallium, which extends from rostral to caudal levels. Thus, the neocortex homolog cannot be found in the classical reptilian dorsal cortex, but perhaps in a small Emx1‐expressing/Lhx9‐negative area at the front of the telencephalon, resembling the avian hyperpallium. The ventral pallium, expressing Lhx9, but not Emx1, gives rise to the dorsal ventricular ridge and appears comparable to the avian nidopallium. We also identified a distinct ventrocaudal pallial sector comparable to the avian arcopallium and to part of the mammalian pallial amygdala. These data open new venues for understanding the organization and evolution of the pallium.
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Affiliation(s)
- Ester Desfilis
- Laboratory of Evolutionary and Developmental Neurobiology, Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), 25198, Lleida, Spain
| | - Antonio Abellán
- Laboratory of Evolutionary and Developmental Neurobiology, Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), 25198, Lleida, Spain
| | - Vicente Sentandreu
- Servicio Central de Apoyo a la Investigación Experimental (SCSIE), Sección de Genómica, University of València, 46100, València, Spain
| | - Loreta Medina
- Laboratory of Evolutionary and Developmental Neurobiology, Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), 25198, Lleida, Spain
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155
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Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol 2017; 1:1722-1730. [PMID: 28963548 DOI: 10.1038/s41559-017-0318-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/16/2017] [Indexed: 02/06/2023]
Abstract
Despite morphological diversification of chordates over 550 million years of evolution, their shared basic anatomical pattern (or 'bodyplan') remains conserved by unknown mechanisms. The developmental hourglass model attributes this to phylum-wide conserved, constrained organogenesis stages that pattern the bodyplan (the phylotype hypothesis); however, there has been no quantitative testing of this idea with a phylum-wide comparison of species. Here, based on data from early-to-late embryonic transcriptomes collected from eight chordates, we suggest that the phylotype hypothesis would be better applied to vertebrates than chordates. Furthermore, we found that vertebrates' conserved mid-embryonic developmental programmes are intensively recruited to other developmental processes, and the degree of the recruitment positively correlates with their evolutionary conservation and essentiality for normal development. Thus, we propose that the intensively recruited genetic system during vertebrates' organogenesis period imposed constraints on its diversification through pleiotropic constraints, which ultimately led to the common anatomical pattern observed in vertebrates.
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156
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Lauber C, Seitz S, Mattei S, Suh A, Beck J, Herstein J, Börold J, Salzburger W, Kaderali L, Briggs JAG, Bartenschlager R. Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses. Cell Host Microbe 2017; 22:387-399.e6. [PMID: 28867387 PMCID: PMC5604429 DOI: 10.1016/j.chom.2017.07.019] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/10/2017] [Accepted: 07/29/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras. Nackednaviruses are non-enveloped fish viruses related to hepadnaviruses Both virus families separated from a common ancestor >400 million years ago The envelope protein gene of hepadnaviruses emerged through two distinct processes Hepadnaviruses mainly co-evolve with hosts while nackednaviruses jump between hosts
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Affiliation(s)
- Chris Lauber
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, 01307 Dresden, Germany
| | - Stefan Seitz
- University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany.
| | - Simone Mattei
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, 75236 Uppsala, Sweden
| | - Jürgen Beck
- Department of Internal Medicine 2/Molecular Biology, University Hospital Freiburg, 79106 Freiburg, Germany
| | - Jennifer Herstein
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jacob Börold
- University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany
| | | | - Lars Kaderali
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, 01307 Dresden, Germany; Institute for Bioinformatics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ralf Bartenschlager
- University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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157
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Moustakas-Verho JE, Cebra-Thomas J, Gilbert SF. Patterning of the turtle shell. Curr Opin Genet Dev 2017; 45:124-131. [DOI: 10.1016/j.gde.2017.03.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/06/2017] [Accepted: 03/21/2017] [Indexed: 12/30/2022]
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158
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Irie N. Remaining questions related to the hourglass model in vertebrate evolution. Curr Opin Genet Dev 2017; 45:103-107. [DOI: 10.1016/j.gde.2017.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/28/2017] [Accepted: 04/13/2017] [Indexed: 12/11/2022]
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159
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Shaffer HB, McCartney-Melstad E, Near TJ, Mount GG, Spinks PQ. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Mol Phylogenet Evol 2017; 115:7-15. [PMID: 28711671 DOI: 10.1016/j.ympev.2017.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/30/2017] [Accepted: 07/10/2017] [Indexed: 10/19/2022]
Abstract
Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5-157.3Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66mya.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
| | - Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Genevieve G Mount
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences, Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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160
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Gao J, Li Q, Wang Z, Zhou Y, Martelli P, Li F, Xiong Z, Wang J, Yang H, Zhang G. Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. Gigascience 2017; 6:1-6. [PMID: 28595343 PMCID: PMC5569961 DOI: 10.1093/gigascience/gix041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/22/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
The Chinese crocodile lizard, Shinisaurus crocodilurus, is the only living representative of the monotypic family Shinisauridae under the order Squamata. It is an obligate semi-aquatic, viviparous, diurnal species restricted to specific portions of mountainous locations in southwestern China and northeastern Vietnam. However, in the past several decades, this species has undergone a rapid decrease in population size due to illegal poaching and habitat disruption, making this unique reptile species endangered and listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Appendix II since 1990. A proposal to uplist it to Appendix I was passed at the Convention on International Trade in Endangered Species of Wild Fauna and Flora Seventeenth meeting of the Conference of the Parties in 2016. To promote the conservation of this species, we sequenced the genome of a male Chinese crocodile lizard using a whole-genome shotgun strategy on the Illumina HiSeq 2000 platform. In total, we generated ∼291 Gb of raw sequencing data (×149 depth) from 13 libraries with insert sizes ranging from 250 bp to 40 kb. After filtering for polymerase chain reaction-duplicated and low-quality reads, ∼137 Gb of clean data (×70 depth) were obtained for genome assembly. We yielded a draft genome assembly with a total length of 2.24 Gb and an N50 scaffold size of 1.47 Mb. The assembled genome was predicted to contain 20 150 protein-coding genes and up to 1114 Mb (49.6%) of repetitive elements. The genomic resource of the Chinese crocodile lizard will contribute to deciphering the biology of this organism and provides an essential tool for conservation efforts. It also provides a valuable resource for future study of squamate evolution.
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Affiliation(s)
- Jian Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qiye Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zongji Wang
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Yang Zhou
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Paolo Martelli
- Veterinary Department, Ocean Park Hong Kong, Hong Kong SAR
| | - Fang Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zijun Xiong
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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161
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Tollis M, DeNardo DF, Cornelius JA, Dolby GA, Edwards T, Henen BT, Karl AE, Murphy RW, Kusumi K. The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species. PLoS One 2017; 12:e0177708. [PMID: 28562605 PMCID: PMC5451010 DOI: 10.1371/journal.pone.0177708] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/02/2017] [Indexed: 12/30/2022] Open
Abstract
Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.
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Affiliation(s)
- Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - John A. Cornelius
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Taylor Edwards
- University of Arizona Genetics Core, University of Arizona, Tucson, Arizona, United States of America
| | - Brian T. Henen
- Natural Resources and Environmental Affairs, Marine Air Ground Task Force Training Command, Marine Corps Air Ground Combat Center, Twentynine Palms, California, United States of America
| | - Alice E. Karl
- Alice E. Karl and Associates, Davis, California, United States of America
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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162
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Poelmann RE, Gittenberger-de Groot AC, Biermans MWM, Dolfing AI, Jagessar A, van Hattum S, Hoogenboom A, Wisse LJ, Vicente-Steijn R, de Bakker MAG, Vonk FJ, Hirasawa T, Kuratani S, Richardson MK. Outflow tract septation and the aortic arch system in reptiles: lessons for understanding the mammalian heart. EvoDevo 2017; 8:9. [PMID: 28491275 PMCID: PMC5424407 DOI: 10.1186/s13227-017-0072-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cardiac outflow tract patterning and cell contribution are studied using an evo-devo approach to reveal insight into the development of aorto-pulmonary septation. RESULTS We studied embryonic stages of reptile hearts (lizard, turtle and crocodile) and compared these to avian and mammalian development. Immunohistochemistry allowed us to indicate where the essential cell components in the outflow tract and aortic sac were deployed, more specifically endocardial, neural crest and second heart field cells. The neural crest-derived aorto-pulmonary septum separates the pulmonary trunk from both aortae in reptiles, presenting with a left visceral and a right systemic aorta arising from the unseptated ventricle. Second heart field-derived cells function as flow dividers between both aortae and between the two pulmonary arteries. In birds, the left visceral aorta disappears early in development, while the right systemic aorta persists. This leads to a fusion of the aorto-pulmonary septum and the aortic flow divider (second heart field population) forming an avian aorto-pulmonary septal complex. In mammals, there is also a second heart field-derived aortic flow divider, albeit at a more distal site, while the aorto-pulmonary septum separates the aortic trunk from the pulmonary trunk. As in birds there is fusion with second heart field-derived cells albeit from the pulmonary flow divider as the right 6th pharyngeal arch artery disappears, resulting in a mammalian aorto-pulmonary septal complex. In crocodiles, birds and mammals, the main septal and parietal endocardial cushions receive neural crest cells that are functional in fusion and myocardialization of the outflow tract septum. Longer-lasting septation in crocodiles demonstrates a heterochrony in development. In other reptiles with no indication of incursion of neural crest cells, there is either no myocardialized outflow tract septum (lizard) or it is vestigial (turtle). Crocodiles are unique in bearing a central shunt, the foramen of Panizza, between the roots of both aortae. Finally, the soft-shell turtle investigated here exhibits a spongy histology of the developing carotid arteries supposedly related to regulation of blood flow during pharyngeal excretion in this species. CONCLUSIONS This is the first time that is shown that an interplay of second heart field-derived flow dividers with a neural crest-derived cell population is a variable but common, denominator across all species studied for vascular patterning and outflow tract septation. The observed differences in normal development of reptiles may have impact on the understanding of development of human congenital outflow tract malformations.
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Affiliation(s)
- Robert E Poelmann
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands.,Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | | | - Marcel W M Biermans
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | - Anne I Dolfing
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | - Armand Jagessar
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | - Sam van Hattum
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | - Amanda Hoogenboom
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | - Lambertus J Wisse
- Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands
| | - Rebecca Vicente-Steijn
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands.,Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands
| | - Merijn A G de Bakker
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
| | - Freek J Vonk
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands.,Naturalis Biodiversity Center, Darwinweg 2, Leiden, The Netherlands
| | - Tatsuya Hirasawa
- Laboratory for Evolutionary Morphology, RIKEN, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Michael K Richardson
- Animal Sciences and Health, Sylvius Laboratories, University of Leiden, Sylviusweg 72, Leiden, The Netherlands
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163
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Liu T, Wang L, Chen H, Huang Y, Yang P, Ahmed N, Wang T, Liu Y, Chen Q. Molecular and Cellular Mechanisms of Apoptosis during Dissociated Spermatogenesis. Front Physiol 2017; 8:188. [PMID: 28424629 PMCID: PMC5372796 DOI: 10.3389/fphys.2017.00188] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/13/2017] [Indexed: 12/12/2022] Open
Abstract
Apoptosis is a tightly controlled process by which tissues eliminate unwanted cells. Spontaneous germ cell apoptosis in testis has been broadly investigated in mammals that have an associated spermatogenesis pattern. However, the mechanism of germ cell apoptosis in seasonally breeding reptiles following a dissociated spermatogenesis has remained enigmatic. In the present study, morphological evidence has clearly confirmed the dissociated spermatogenesis pattern in Pelodiscus sinensis. TUNEL and TEM analyses presented dynamic changes and ultrastructural characteristics of apoptotic germ cells during seasonal spermatogenesis, implying that apoptosis might be one of the key mechanisms to clear degraded germ cells. Furthermore, using RNA-Seq and digital gene expression (DGE) profiling, a large number of apoptosis-related differentially expressed genes (DEGs) at different phases of spermatogenesis were identified and characterized in the testis. DGE and RT-qPCR analysis revealed that the critical anti-apoptosis genes, such as Bcl-2, BAG1, and BAG5, showed up-regulated patterns during intermediate and late spermatogenesis. Moreover, the increases in mitochondrial transmembrane potential in July and October were detected by JC-1 staining. Notably, the low protein levels of pro-apoptotic cleaved caspase-3 and CytC in cytoplasm were detected by immunohistochemistry and western blot analyses, indicating that the CytC-Caspase model might be responsible for the effects of germ cell apoptosis on seasonal spermatogenesis. These results facilitate understanding the regulatory mechanisms of apoptosis during spermatogenesis and uncovering the biological process of the dissociated spermatogenesis system in reptiles.
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Affiliation(s)
- Tengfei Liu
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Lingling Wang
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Hong Chen
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Yufei Huang
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Ping Yang
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Nisar Ahmed
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Taozhi Wang
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Yi Liu
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
| | - Qiusheng Chen
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
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164
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Drost HG, Janitza P, Grosse I, Quint M. Cross-kingdom comparison of the developmental hourglass. Curr Opin Genet Dev 2017; 45:69-75. [PMID: 28347942 DOI: 10.1016/j.gde.2017.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/02/2017] [Indexed: 01/01/2023]
Abstract
The developmental hourglass model has its foundations in classic anatomical studies by von Baer and Haeckel. In this context, even the conservation of animal body plans has been explained by evolutionary constraints acting on mid-embryogenic development. Recent studies have shown that developmental hourglass patterns also exist on the transcriptomic level, mirroring the corresponding morphological patterns. The identification of similar patterns in embryonic, post-embryonic, and life cycle spanning transcriptomes in plant and fungus development, however, contradict the notion of a direct coupling between morphological and molecular patterns. To explain the existence of hourglass patterns across kingdoms and developmental processes, we propose the organizational checkpoint model that integrates the developmental hourglass model into a framework of transcriptome switches.
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Affiliation(s)
- Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Philipp Janitza
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
| | - Ivo Grosse
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany; German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Marcel Quint
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany.
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165
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Radhakrishnan S, Literman R, Neuwald J, Severin A, Valenzuela N. Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development. PLoS One 2017; 12:e0172044. [PMID: 28296881 PMCID: PMC5352168 DOI: 10.1371/journal.pone.0172044] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/30/2017] [Indexed: 12/24/2022] Open
Abstract
Vertebrate sexual fate is decided primarily by the individual's genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera-GSD), to test whether TSD's and GSD's transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle gonadogenesis, but their transcription is generally more thermoresponsive in TSD than GSD, and concordant with their sex-specific function in mammals [e.g., upregulation of Amh, Ar, Esr1, Fog2, Gata4, Igf1r, Insr, and Lhx9 at male-producing temperature, and of β-catenin, Foxl2, Aromatase (Cyp19a1), Fst, Nf-kb, Crabp2 at female-producing temperature in Chrysemys]. Notably, antagonistic elements in gonadogenesis (e.g., β-catenin and Insr) were thermosensitive only in TSD early-embryos. Cirbp showed warm-temperature upregulation in both turtles disputing its purported key TSD role. Genes that may convert thermal inputs into sex-specific development (e.g., signaling and hormonal pathways, RNA-binding and heat-shock) were differentially regulated. Jak-Stat, Nf-κB, retinoic-acid, Wnt, and Mapk-signaling (not Akt and Ras-signaling) potentially mediate TSD thermosensitivity. Numerous species-specific ncRNAs (including Xist) were differentially-expressed, mostly upregulated at colder temperatures, as were unannotated loci that constitute novel TSD candidates. Cirbp showed warm-temperature upregulation in both turtles. Consistent transcription between turtles and alligator revealed putatively-critical reptilian TSD elements for male (Sf1, Amh, Amhr2) and female (Crabp2 and Hspb1) gonadogenesis. In conclusion, while preliminary, our data helps illuminate the regulation and evolution of vertebrate sex determination, and contribute genomic resources to guide further research into this fundamental biological process.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States of America
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Robert Literman
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
- Ecology and Evolutionary Biology Program, Iowa State University, Ames, IA, United States of America
| | - Jennifer Neuwald
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Andrew Severin
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
- Genome Informatics Facility, Iowa State University, Ames, IA, United States of America
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
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166
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De novo transcriptome analysis reveals insights into different mechanisms of growth and immunity in a Chinese soft-shelled turtle hybrid and the parental varieties. Gene 2017; 605:54-62. [DOI: 10.1016/j.gene.2016.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/22/2016] [Accepted: 12/05/2016] [Indexed: 12/16/2022]
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167
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Literman R, Radhakrishnan S, Tamplin J, Burke R, Dresser C, Valenzuela N. Development of sexing primers in Glyptemys insculpta and Apalone spinifera turtles uncovers an XX/XY sex-determining system in the critically-endangered bog turtle Glyptemys muhlenbergii. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0711-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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168
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Pantalacci S, Guéguen L, Petit C, Lambert A, Peterkovà R, Sémon M. Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology. Genome Biol 2017; 18:29. [PMID: 28202034 PMCID: PMC5312534 DOI: 10.1186/s13059-017-1157-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/19/2017] [Indexed: 11/10/2022] Open
Abstract
Background Comparative transcriptomics can answer many questions in developmental and evolutionary developmental biology. Most transcriptomic studies start by showing global patterns of variation in transcriptomes that differ between species or organs through developmental time. However, little is known about the kinds of expression differences that shape these patterns. Results We compared transcriptomes during the development of two morphologically distinct serial organs, the upper and lower first molars of the mouse. We found that these two types of teeth largely share the same gene expression dynamics but that three major transcriptomic signatures distinguish them, all of which are shaped by differences in the relative abundance of different cell types. First, lower/upper molar differences are maintained throughout morphogenesis and stem from differences in the relative abundance of mesenchyme and from constant differences in gene expression within tissues. Second, there are clear time-shift differences in the transcriptomes of the two molars related to cusp tissue abundance. Third, the transcriptomes differ most during early-mid crown morphogenesis, corresponding to exaggerated morphogenetic processes in the upper molar involving fewer mitotic cells but more migrating cells. From these findings, we formulate hypotheses about the mechanisms enabling the two molars to reach different phenotypes. We also successfully applied our approach to forelimb and hindlimb development. Conclusions Gene expression in a complex tissue reflects not only transcriptional regulation but also abundance of different cell types. This knowledge provides valuable insights into the cellular processes underpinning differences in organ development. Our approach should be applicable to most comparative developmental contexts. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1157-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Pantalacci
- UnivLyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratoire de Biologie et Modélisation de la Cellule, 15 parvis Descartes, F-69007, Lyon, France.
| | - Laurent Guéguen
- Laboratoire de Biométrie et Biologie Évolutive (LBBE), Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Coraline Petit
- UnivLyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratoire de Biologie et Modélisation de la Cellule, 15 parvis Descartes, F-69007, Lyon, France
| | - Anne Lambert
- UnivLyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratoire de Biologie et Modélisation de la Cellule, 15 parvis Descartes, F-69007, Lyon, France
| | - Renata Peterkovà
- Department of Teratology, Institute of Experimental Medicine, Academy of Sciences AS CR, Videnska 1083, 142 20, Prague, Czech Republic
| | - Marie Sémon
- UnivLyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratoire de Biologie et Modélisation de la Cellule, 15 parvis Descartes, F-69007, Lyon, France.
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169
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Rovatsos M, Praschag P, Fritz U, Kratochvšl L. Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae). Sci Rep 2017; 7:42150. [PMID: 28186115 PMCID: PMC5301483 DOI: 10.1038/srep42150] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/05/2017] [Indexed: 01/18/2023] Open
Abstract
Turtles demonstrate variability in sex determination ranging from environmental sex determination (ESD) to highly differentiated sex chromosomes. However, the evolutionary dynamics of sex determining systems in this group is not well known. Differentiated ZZ/ZW sex chromosomes were identified in two species of the softshell turtles (Trionychidae) from the subfamily Trionychinae and Z-specific genes were identified in a single species. We tested Z-specificity of a subset of these genes by quantitative PCR comparing copy gene numbers in male and female genomes in 10 species covering the phylogenetic diversity of trionychids. We demonstrated that differentiated ZZ/ZW sex chromosomes are conserved across the whole family and that they were already present in the common ancestor of the extant trionychids. As the sister lineage, Carettochelys insculpta, possess ESD, we can date the origin of the sex chromosomes in trionychids between 200 Mya (split of Trionychidae and Carettochelyidae) and 120 Mya (basal splitting of the recent trionychids). The results support the evolutionary stability of differentiated sex chromosomes in some lineages of ectothermic vertebrates. Moreover, our approach determining sex-linkage of protein coding genes can be used as a reliable technique of molecular sexing across trionychids useful for effective breeding strategy in conservation projects of endangered species.
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Affiliation(s)
- Michail Rovatsos
- Faculty of Science, Charles University, Department of Ecology, Viničná 7, 12844 Praha 2, Czech Republic
| | - Peter Praschag
- Turtle Island, Turtle Conservation Center, Am Katzelbach 98, 8054 Graz, Austria
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Lukáš Kratochvšl
- Faculty of Science, Charles University, Department of Ecology, Viničná 7, 12844 Praha 2, Czech Republic
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170
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Silva L, Antunes A. Vomeronasal Receptors in Vertebrates and the Evolution of Pheromone Detection. Annu Rev Anim Biosci 2017; 5:353-370. [DOI: 10.1146/annurev-animal-022516-022801] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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171
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Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nat Commun 2017; 8:14229. [PMID: 28165450 PMCID: PMC5473641 DOI: 10.1038/ncomms14229] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 12/12/2016] [Indexed: 01/01/2023] Open
Abstract
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers. By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions. Many ASHCEs show differential histone modifications that may participate in regulation of limb development. Comparative embryonic gene expression analyses across tetrapod species suggest ASHCE-associated genes have unique roles in developing avian limbs. In particular, we demonstrate how the ASHCE driven avian-specific expression of gene Sim1 driven by ASHCE may be associated with the evolution and development of flight feathers. Together, these findings demonstrate regulatory roles of ASHCEs in the creation of avian-specific traits, and further highlight the importance of cis-regulatory rewiring during macroevolutionary changes.
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172
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Pham T, Day SM, Glassford WJ, Williams TM, Rebeiz M. The evolutionary origination of a novel expression pattern through an extreme heterochronic shift. Evol Dev 2017; 19:43-55. [PMID: 28116844 DOI: 10.1111/ede.12215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The evolutionary origins of morphological structures are thought to often depend upon the redeployment of old genes into new developmental settings. Although many examples of cis-regulatory divergence have shown how pre-existing patterns of gene expression have been altered, only a small number of case studies have traced the origins of cis-regulatory elements that drive new expression domains. Here, we elucidate the evolutionary history of a novel expression pattern of the yellow gene within the Zaprionus genus of fruit flies. We observed a unique pattern of yellow transcript accumulation in the wing disc during the third larval instar, a stage that precedes its typical expression pattern associated with cuticular melanization by about a week. The region of the Zaprionus wing disc that expresses yellow subsequently develops into a portion of the thorax, a tissue for which yellow expression has been reported for several fruit fly species. Tests of GFP reporter transgenes containing the Zaprionus yellow regulatory region revealed that the wing disc pattern arose by changes in the cis-regulatory region of yellow. Moreover, the wing disc enhancer activity of yellow depends upon a short conserved sequence with ancestral thoracic functions, suggesting that the pupal thorax regulatory sequence was genetically reprogrammed to drive expression that commences much earlier during development. These results highlight how novel domains of gene expression may arise by extreme shifts in timing during the origins of novel traits.
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Affiliation(s)
- Thomas Pham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephanie M Day
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - William J Glassford
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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173
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Sotero-Caio CG, Platt RN, Suh A, Ray DA. Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biol Evol 2017; 9:161-177. [PMID: 28158585 PMCID: PMC5381603 DOI: 10.1093/gbe/evw264] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.
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Affiliation(s)
| | - Roy N. Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
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174
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Hou PS, Kumamoto T, Hanashima C. A Sensitive and Versatile In Situ Hybridization Protocol for Gene Expression Analysis in Developing Amniote Brains. Methods Mol Biol 2017; 1650:319-334. [PMID: 28809032 DOI: 10.1007/978-1-4939-7216-6_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The detection of specific RNA molecules in embryonic tissues has wide research applications including studying gene expression dynamics in brain development and evolution. Recent advances in sequencing technologies have introduced new animal models to explore the molecular principles underlying the assembly and diversification of brain circuits between different amniote species. Here, we provide a step-by-step protocol for a versatile in situ hybridization method that is immediately applicable to a range of amniote embryos including zebra finch and Madagascar ground gecko, two new model organisms that have rapidly emerged for comparative brain studies over recent years. The sensitive detection of transcripts from low to high abundance expression range using the same platform enables direct comparison of gene of interest among different amniotes, providing high-resolution spatiotemporal information of gene expression to dissect the molecular principles underlying brain evolution.
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Affiliation(s)
- Pei-Shan Hou
- Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, Kobe, 650-0047, Japan
| | - Takuma Kumamoto
- Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, Kobe, 650-0047, Japan
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, 75012, Paris, France
| | - Carina Hanashima
- Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, Kobe, 650-0047, Japan.
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan.
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175
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Pujiastuti DY, Shih YH, Chen WL, Sukoso, Hsu JL. Screening of angiotensin-I converting enzyme inhibitory peptides derived from soft-shelled turtle yolk using two orthogonal bioassay-guided fractionations. J Funct Foods 2017. [DOI: 10.1016/j.jff.2016.10.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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176
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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177
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Xu C, Grizante MB, Kusumi K. Somitogenesis and Axial Development in Reptiles. Methods Mol Biol 2017; 1650:335-353. [PMID: 28809033 DOI: 10.1007/978-1-4939-7216-6_23] [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] [Indexed: 06/07/2023]
Abstract
Among amniote vertebrates, reptiles display the greatest variation in axial skeleton morphology. Only recently have they been used in gene expression studies of somitogenesis , challenging previous assumptions about the segmentation clock and axial patterning. An increasing number of reptile genomes and transcriptomes are becoming available as next-generation sequencing becomes more affordable. Information regarding gene sequence and structure can be used to design and synthesize labeled riboprobes by in vitro transcription for gene expression analysis by in situ hybridization, thus, enabling the characterization of spatial and temporal expression patterns of genes involved in somitogenesis, a topic of great interest within evolutionary developmental studies of vertebrates.
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Affiliation(s)
- Cindy Xu
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Mariana B Grizante
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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178
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Iverson JB, Klondaris H, Angell CS, Tori WP. Olfaction as a Cue for Nest-Site Choice in Turtles. CHELONIAN CONSERVATION AND BIOLOGY 2016. [DOI: 10.2744/ccb-1199.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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179
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Xiong Z, Li F, Li Q, Zhou L, Gamble T, Zheng J, Kui L, Li C, Li S, Yang H, Zhang G. Draft genome of the leopard gecko, Eublepharis macularius. Gigascience 2016; 5:47. [PMID: 27784328 PMCID: PMC5080775 DOI: 10.1186/s13742-016-0151-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 10/11/2016] [Indexed: 01/21/2023] Open
Abstract
Background Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these ‘rules’ and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in ‘typical’ geckos. Findings We report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs. Conclusions Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0151-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zijun Xiong
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
| | - Fang Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA
| | - Jiao Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shengbin Li
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. .,Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
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180
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Zhou Y, Liang Q, Li W, Gu Y, Liao X, Fang W, Li X. Characterization and functional analysis of toll-like receptor 4 in Chinese soft-shelled turtle Pelodiscus sinensis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 63:128-135. [PMID: 27259833 DOI: 10.1016/j.dci.2016.05.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 06/05/2023]
Abstract
Mammalian Toll-like receptor 4 (TLR4) recognizes lipopolysaccharide (LPS) in initiating the innate immune responses. Early studies indicate that turtles are more resistant to LPS challenge than mammals. It remains unknown if turtles express TLR4 and why they are more resistant to LPS. In this study, TLR4 gene from Chinese soft-shelled turtle, Pelodiscus sinensis, was cloned and characterized. The full length cDNA of turtle TLR4 (tTLR4) consists of 3396 base pairs with an 2499-bp open reading frame, encoding 833 amino acids. Phylogenetic and syntenic analyses suggest that tTLR4 is to be orthologous to human TLR4. Its mRNA expression was up-regulated in spleen and blood of turtles upon Aeromonas hydrophila infection. Stimulation of turtle peripheral blood monocytes with LPS significantly upregulated tTLR4 mRNA and inflammation-related gene expression, such as Interleukin-1β (IL-1β) and cyclooxygenase-2 (COX-2). In tTLR4-expressing HEK293 cells, higher concentration of LPS exposure could enhance the activity of the NF-κB promoter, but not the INF-β promoter. Such activity required co-expression of turtle myeloid differentiation factor 2 (tMD2) and cluster of differentiation 14 (tCD14). These results provide evidence for a functional TLR4 in reptiles and, together with the syntenic analysis, support the idea that the TLR4 receptor for LPS recognition may have arisen after reptiles.
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Affiliation(s)
- Yingshan Zhou
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Quan Liang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Weifen Li
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yuanxing Gu
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xun Liao
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Weihuan Fang
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiaoliang Li
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
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181
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Liu T, Yang P, Chen H, Huang Y, Liu Y, Waqas Y, Ahmed N, Chu X, Chen Q. Global analysis of differential gene expression related to long-term sperm storage in oviduct of Chinese Soft-Shelled Turtle Pelodiscus sinensis. Sci Rep 2016; 6:33296. [PMID: 27628424 PMCID: PMC5024102 DOI: 10.1038/srep33296] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/24/2016] [Indexed: 12/19/2022] Open
Abstract
Important evolutionary and ecological consequences arise from the ability of female turtles to store viable spermatozoa for an extended period. Although previous morphological studies have observed the localization of spermatozoa in Pelodiscus sinensis oviduct, no systematic study on the identification of genes that are involved in long-term sperm storage has been performed. In this study, the oviduct of P. sinensis at different phases (reproductive and hibernation seasons) was prepared for RNA-Seq and gene expression profiling. In total, 2,662 differentially expressed genes (DEGs) including 1,224 up- and 1,438 down-regulated genes were identified from two cDNA libraries. Functional enrichment analysis indicated that many genes were predominantly involved in the immune response, apoptosis pathway and regulation of autophagy. RT-qPCR, ELISA, western blot and IHC analyses showed that the expression profiles of mRNA and protein in selected DEGs were in consistent with results from RNA-Seq analysis. Remarkably, TUNEL analysis revealed the reduced number of apoptotic cells during sperm storage. IHC and TEM analyses found that autophagy occurred in the oviduct epithelial cells, where the spermatozoa were closely attached. The outcomes of this study provide fundamental insights into the complex sperm storage regulatory process and facilitate elucidating the mechanism of sperm storage in P. sinensis.
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Affiliation(s)
- Tengfei Liu
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Ping Yang
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Hong Chen
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yufei Huang
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yi Liu
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yasir Waqas
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Nisar Ahmed
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Xiaoya Chu
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Qiusheng Chen
- Laboratory of Animal Cell Biology and Embryology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
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182
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Li M, Yeung CKL, Tian S, Zhou X, Lin Y, Li X, Li R. Reply to 'Olfactory genes in Tibetan wild boar (NG-CR42819)'. Nat Genet 2016; 48:973-4. [PMID: 27573683 DOI: 10.1038/ng.3639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | | | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yu Lin
- Novogene Bioinformatics Institute, Beijing, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
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183
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Gredler ML. Developmental and Evolutionary Origins of the Amniote Phallus. Integr Comp Biol 2016; 56:694-704. [DOI: 10.1093/icb/icw102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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184
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Alfaro-Núñez A, Bojesen AM, Bertelsen MF, Wales N, Balazs GH, Gilbert MTP. Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles. PeerJ 2016; 4:e2274. [PMID: 27547576 PMCID: PMC4974929 DOI: 10.7717/peerj.2274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023] Open
Abstract
The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.
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Affiliation(s)
- Alonzo Alfaro-Núñez
- Section for Evolutionary Genomics, Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark; Laboratorio de Biomedicina, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Veterinary Clinical Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen , Frederiskberg , Copenhagen , Denmark
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo , Frederiskberg , Copenhagen , Denmark
| | - Nathan Wales
- Section for Evolutionary Genomics, Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen , Copenhagen K , Denmark
| | - George H Balazs
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service , Honolulu , HI , United States of America
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark; Trace and Environmental DNA Laboratory, School of Environment and Agriculture, Curtin University of Technology, Perth, Perth, Australia
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185
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Grone BP, Maruska KP. Three Distinct Glutamate Decarboxylase Genes in Vertebrates. Sci Rep 2016; 6:30507. [PMID: 27461130 PMCID: PMC4962313 DOI: 10.1038/srep30507] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/04/2016] [Indexed: 11/14/2022] Open
Abstract
Gamma-aminobutyric acid (GABA) is a widely conserved signaling molecule that in animals has been adapted as a neurotransmitter. GABA is synthesized from the amino acid glutamate by the action of glutamate decarboxylases (GADs). Two vertebrate genes, GAD1 and GAD2, encode distinct GAD proteins: GAD67 and GAD65, respectively. We have identified a third vertebrate GAD gene, GAD3. This gene is conserved in fishes as well as tetrapods. We analyzed protein sequence, gene structure, synteny, and phylogenetics to identify GAD3 as a homolog of GAD1 and GAD2. Interestingly, we found that GAD3 was lost in the hominid lineage. Because of the importance of GABA as a neurotransmitter, GAD3 may play important roles in vertebrate nervous systems.
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Affiliation(s)
- Brian P. Grone
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Karen P. Maruska
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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186
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Irisarri I, Meyer A. The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes. Syst Biol 2016; 65:1057-1075. [PMID: 27425642 DOI: 10.1093/sysbio/syw057] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/08/2016] [Indexed: 01/08/2023] Open
Abstract
Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error.].
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Affiliation(s)
- Iker Irisarri
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Axel Meyer
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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187
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Montiel EE, Badenhorst D, Lee LS, Literman R, Trifonov V, Valenzuela N. Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes. Cytogenet Genome Res 2016; 148:292-304. [DOI: 10.1159/000447478] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
Turtle karyotypes are highly conserved compared to other vertebrates; yet, variation in diploid number (2n = 26-68) reflects profound genomic reorganization, which correlates with evolutionary turnovers in sex determination. We evaluate the published literature and newly collected comparative cytogenetic data (G- and C-banding, 18S-NOR, and telomere-FISH mapping) from 13 species spanning 2n = 28-68 to revisit turtle genome evolution and sex determination. Interstitial telomeric sites were detected in multiple lineages that underwent diploid number and sex determination turnovers, suggesting chromosomal rearrangements. C-banding revealed potential interspecific variation in centromere composition and interstitial heterochromatin at secondary constrictions. 18S-NORs were detected in secondary constrictions in a single chromosomal pair per species, refuting previous reports of multiple NORs in turtles. 18S-NORs are linked to ZW chromosomes in Apalone and Pelodiscus and to X (not Y) in Staurotypus. Notably, comparative genomics across amniotes revealed that the sex chromosomes of several turtles, as well as mammals and some lizards, are homologous to components of Xenopus tropicalis XTR1 (carrying Dmrt1). Other turtle sex chromosomes are homologous to XTR4 (carrying Wt1). Interestingly, all known turtle sex chromosomes, except in Trionychidae, evolved via inversions around Dmrt1 or Wt1. Thus, XTR1 appears to represent an amniote proto-sex chromosome (perhaps linked ancestrally to XTR4) that gave rise to turtle and other amniote sex chromosomes.
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188
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Yoshida M, Kajikawa E, Kurokawa D, Noro M, Iwai T, Yonemura S, Kobayashi K, Kiyonari H, Aizawa S. Conserved and divergent expression patterns of markers of axial development in reptilian embryos: Chinese soft-shell turtle and Madagascar ground gecko. Dev Biol 2016; 415:122-142. [DOI: 10.1016/j.ydbio.2016.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 12/18/2022]
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189
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Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development. Gene 2016; 591:393-402. [PMID: 27320726 DOI: 10.1016/j.gene.2016.06.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 01/12/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level. Previous studies have shown that miRNA regulation contributes to a diverse set of processes including cellular differentiation and morphogenesis which leads to the creation of different cell types in multicellular organisms and is thus key to animal development. Feathers are one of the most distinctive features of extant birds and are important for multiple functions including flight, thermal regulation, and sexual selection. However, the role of miRNAs in feather development has been woefully understudied despite the identification of cell signaling pathways, cell adhesion molecules and structural genes involved in feather development. In this study, we performed a microarray experiment comparing the expression of miRNAs and mRNAs among three embryonic stages of development and two tissues (scutate scale and feather) of the chicken. We combined this expression data with miRNA target prediction tools and a curated list of feather related genes to produce a set of 19 miRNA-mRNA duplexes. These targeted mRNAs have been previously identified as important cell signaling and cell adhesion genes as well as structural genes involved in feather and scale morphogenesis. Interestingly, the miRNA target site of the cell signaling pathway gene, Aldehyde Dehydrogenase 1 Family, Member A3 (ALDH1A3), is unique to birds indicating a novel role in Aves. The identified miRNA target site of the cell adhesion gene, Tenascin C (TNC), is only found in specific chicken TNC splice variants that are differentially expressed in developing scutate scale and feather tissue indicating an important role of miRNA regulation in epidermal differentiation. Additionally, we found that β-keratins, a major structural component of avian and reptilian epidermal appendages, are targeted by multiple miRNA genes. In conclusion, our work provides quantitative expression data on miRNAs and mRNAs during feather and scale development and has produced a highly diverse, but manageable list of miRNA-mRNA duplexes for future validation experiments.
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190
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Matsubara Y, Kuroiwa A, Suzuki T. Efficient harvesting methods for early-stage snake and turtle embryos. Dev Growth Differ 2016; 58:241-9. [DOI: 10.1111/dgd.12278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Yoshiyuki Matsubara
- Division of Biological Science; Graduate School of Science; Nagoya University Furo-cho; Chikusa-ku Nagoya 464-8602 Japan
| | - Atsushi Kuroiwa
- Division of Biological Science; Graduate School of Science; Nagoya University Furo-cho; Chikusa-ku Nagoya 464-8602 Japan
| | - Takayuki Suzuki
- Division of Biological Science; Graduate School of Science; Nagoya University Furo-cho; Chikusa-ku Nagoya 464-8602 Japan
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191
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Priyam M, Tripathy M, Rai U, Ghorai SM. Tracing the evolutionary lineage of pattern recognition receptor homologues in vertebrates: An insight into reptilian immunity via de novo sequencing of the wall lizard splenic transcriptome. Vet Immunol Immunopathol 2016; 172:26-37. [DOI: 10.1016/j.vetimm.2016.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
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192
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Hanukoglu I, Hanukoglu A. Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. Gene 2016; 579:95-132. [PMID: 26772908 PMCID: PMC4756657 DOI: 10.1016/j.gene.2015.12.061] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/20/2015] [Accepted: 12/22/2015] [Indexed: 01/24/2023]
Abstract
The epithelial sodium channel (ENaC) is composed of three homologous subunits and allows the flow of Na(+) ions across high resistance epithelia, maintaining body salt and water homeostasis. ENaC dependent reabsorption of Na(+) in the kidney tubules regulates extracellular fluid (ECF) volume and blood pressure by modulating osmolarity. In multi-ciliated cells, ENaC is located in cilia and plays an essential role in the regulation of epithelial surface liquid volume necessary for cilial transport of mucus and gametes in the respiratory and reproductive tracts respectively. The subunits that form ENaC (named as alpha, beta, gamma and delta, encoded by genes SCNN1A, SCNN1B, SCNN1G, and SCNN1D) are members of the ENaC/Degenerin superfamily. The earliest appearance of ENaC orthologs is in the genomes of the most ancient vertebrate taxon, Cyclostomata (jawless vertebrates) including lampreys, followed by earliest representatives of Gnathostomata (jawed vertebrates) including cartilaginous sharks. Among Euteleostomi (bony vertebrates), Actinopterygii (ray finned-fishes) branch has lost ENaC genes. Yet, most animals in the Sarcopterygii (lobe-finned fish) branch including Tetrapoda, amphibians and amniotes (lizards, crocodiles, birds, and mammals), have four ENaC paralogs. We compared the sequences of ENaC orthologs from 20 species and established criteria for the identification of ENaC orthologs and paralogs, and their distinction from other members of the ENaC/Degenerin superfamily, especially ASIC family. Differences between ENaCs and ASICs are summarized in view of their physiological functions and tissue distributions. Structural motifs that are conserved throughout vertebrate ENaCs are highlighted. We also present a comparative overview of the genotype-phenotype relationships in inherited diseases associated with ENaC mutations, including multisystem pseudohypoaldosteronism (PHA1B), Liddle syndrome, cystic fibrosis-like disease and essential hypertension.
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Affiliation(s)
- Israel Hanukoglu
- Laboratory of Cell Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel.
| | - Aaron Hanukoglu
- Division of Pediatric Endocrinology, E. Wolfson Medical Center, Holon, Israel; Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
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193
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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194
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Moustakas-Verho JE, Cherepanov GO. The integumental appendages of the turtle shell: an evo-devo perspective. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 324:221-9. [PMID: 25877335 DOI: 10.1002/jez.b.22619] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/26/2015] [Indexed: 12/24/2022]
Abstract
The turtle shell is composed of dorsal armor (carapace) and ventral armor (plastron) covered by a keratinized epithelium. There are two epithelial appendages of the turtle shell: scutes (large epidermal shields separated by furrows and forming a unique mosaic) and tubercles (numerous small epidermal bumps located on the carapaces of some species). In our perspective, we take a synthetic, comparative approach to consider the homology and evolution of these integumental appendages. Scutes have been more intensively studied, as they are autapomorphic for turtles and can be diagnostic taxonomically. Their pattern of tessellation is stable phylogenetically, but labile in the individual. We discuss the history of developmental investigations of these structures and hypotheses of evolutionary and anomalous variation. In our estimation, the scutes of the turtle shell are an evolutionary novelty, whereas the tubercles found on the shells of some turtles are homologous to reptilian scales.
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195
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Coloration reflects skin pterin concentration in a red-tailed lizard. Comp Biochem Physiol B Biochem Mol Biol 2016; 193:17-24. [DOI: 10.1016/j.cbpb.2015.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 12/23/2022]
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196
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Adams RH, Blackmon H, Reyes-Velasco J, Schield DR, Card DC, Andrew AL, Waynewood N, Castoe TA. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome 2016; 59:295-310. [PMID: 27064176 DOI: 10.1139/gen-2015-0124] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.
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Affiliation(s)
- Richard H Adams
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Heath Blackmon
- b Department of Ecology, Evolution & Behavior, 1987 Upper Buford Cir., University of Minnesota, Saint Paul, MN 55108-6097, USA
| | - Jacobo Reyes-Velasco
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Drew R Schield
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Daren C Card
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Audra L Andrew
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Nyimah Waynewood
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Todd A Castoe
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
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197
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Drost HG, Bellstädt J, Ó'Maoiléidigh DS, Silva AT, Gabel A, Weinholdt C, Ryan PT, Dekkers BJW, Bentsink L, Hilhorst HWM, Ligterink W, Wellmer F, Grosse I, Quint M. Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development. Mol Biol Evol 2016; 33:1158-63. [PMID: 26912813 PMCID: PMC4839224 DOI: 10.1093/molbev/msw039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana Here, we investigated whether plant hourglass patterns are also found postembryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.
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Affiliation(s)
- Hajk-Georg Drost
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Julia Bellstädt
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | - Anderson T Silva
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Alexander Gabel
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Claus Weinholdt
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Patrick T Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Bas J W Dekkers
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands Department of Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
| | - Leónie Bentsink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands Department of Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Marcel Quint
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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198
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Vandewege MW, Mangum SF, Gabaldón T, Castoe TA, Ray DA, Hoffmann FG. Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes. Genome Biol Evol 2016; 8:470-80. [PMID: 26865070 PMCID: PMC4825420 DOI: 10.1093/gbe/evw013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and losses. Several studies also suggest that mammalian OR repertoires are influenced by life history traits. Sauropsida is a diverse group of vertebrates group that is the sister group to mammals, and includes birds, testudines, squamates, and crocodilians, and represents a natural system to explore predictions derived from mammalian studies. In this study, we analyzed olfactory receptor (OR) repertoire variation among several representative species and found that the number of intact OR genes in sauropsid genomes analyzed ranged over an order of magnitude, from 108 in the green anole to over 1,000 in turtles. Our results suggest that different sauropsid lineages have highly divergent OR repertoire composition that derive from lineage-specific combinations of gene expansions, losses, and retentions of ancestral OR genes. These differences also suggest that varying degrees of adaption related to life history have shaped the unique OR repertoires observed across sauropsid lineages.
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Affiliation(s)
- Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University
| | - Sarah F Mangum
- Department of Biological Sciences, Texas Tech University
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington
| | - David A Ray
- Department of Biological Sciences, Texas Tech University
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biochemistry, Mississippi State University
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199
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Kohsokabe T, Kaneko K. Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:61-84. [PMID: 26678220 PMCID: PMC5064737 DOI: 10.1002/jez.b.22666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 11/24/2015] [Indexed: 11/12/2022]
Abstract
Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis.
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Affiliation(s)
- Takahiro Kohsokabe
- Department of Basic ScienceGraduate School of Arts and SciencesThe University of TokyoTokyoJapan
| | - Kunihiko Kaneko
- Research Center for Complex Systems BiologyGraduate School of Arts and Sciences The University of TokyoTokyoJapan
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200
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Yatsu R, Miyagawa S, Kohno S, Saito S, Lowers RH, Ogino Y, Fukuta N, Katsu Y, Ohta Y, Tominaga M, Guillette LJ, Iguchi T. TRPV4 associates environmental temperature and sex determination in the American alligator. Sci Rep 2015; 5:18581. [PMID: 26677944 PMCID: PMC4683465 DOI: 10.1038/srep18581] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/20/2015] [Indexed: 12/28/2022] Open
Abstract
Temperature-dependent sex determination (TSD), commonly found among reptiles, is a sex determination mode in which the incubation temperature during a critical temperature sensitive period (TSP) determines sexual fate of the individual rather than the individual’s genotypic background. In the American alligator (Alligator mississippiensis), eggs incubated during the TSP at 33 °C (male producing temperature: MPT) yields male offspring, whereas incubation temperatures below 30 °C (female producing temperature: FPT) lead to female offspring. However, many of the details of the underlying molecular mechanism remains elusive, and the molecular link between environmental temperature and sex determination pathway is yet to be elucidated. Here we show the alligator TRPV4 ortholog (AmTRPV4) to be activated at temperatures proximate to the TSD-related temperature in alligators, and using pharmacological exposure, we show that AmTRPV4 channel activity affects gene expression patterns associated with male differentiation. This is the first experimental demonstration of a link between a well-described thermo-sensory mechanism, TRPV4 channel, and its potential role in regulation of TSD in vertebrates, shedding unique new light on the elusive TSD molecular mechanism.
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Affiliation(s)
- Ryohei Yatsu
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki Aichi 444-8787 Japan.,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan
| | - Shinichi Miyagawa
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki Aichi 444-8787 Japan.,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan
| | - Satomi Kohno
- Department of Obstetrics and Gynecology, Medical University of South Carolina, and Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Charleston SC 29412 USA
| | - Shigeru Saito
- Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan.,Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki Aichi 444-8787 Japan
| | - Russell H Lowers
- Innovative Health Applications, Kennedy Space Center, Merritt Island FL 32899 USA
| | - Yukiko Ogino
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki Aichi 444-8787 Japan.,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan
| | - Naomi Fukuta
- Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan
| | - Yoshinao Katsu
- Graduate School of Life Science and Department of Biological Sciences, Hokkaido University, Sapporo Hokkaido 062-8520 Japan
| | - Yasuhiko Ohta
- Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Koyama Tottori 680-8553 Japan
| | - Makoto Tominaga
- Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan.,Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki Aichi 444-8787 Japan
| | - Louis J Guillette
- Department of Obstetrics and Gynecology, Medical University of South Carolina, and Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Charleston SC 29412 USA
| | - Taisen Iguchi
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki Aichi 444-8787 Japan.,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki Aichi 444-8787 Japan
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