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Srikulnath K, Ahmad SF, Singchat W, Panthum T. Why Do Some Vertebrates Have Microchromosomes? Cells 2021; 10:2182. [PMID: 34571831 PMCID: PMC8466491 DOI: 10.3390/cells10092182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022] Open
Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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Menezes RST, Gazoni T, Costa MA. Cytogenetics of warrior wasps (Vespidae:Synoeca) reveals intense evolutionary dynamics of ribosomal DNA clusters and an unprecedented number of microchromosomes in Hymenoptera. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras – Universidade de São Paulo (FFCLRP/USP), Ribeirão Preto, SP, Brazil
| | - Thiago Gazoni
- Departamento de Biologia – Universidade Estadual Paulista (UNESP), Instituto de Biociências, Rio Claro, SP, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014; 15:1060. [PMID: 25496766 PMCID: PMC4362836 DOI: 10.1186/1471-2164-15-1060] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
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Affiliation(s)
| | - Marta Farré
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Pamela E Lithgow
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Katie E Fowler
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
- />School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, Kent CT1 1QU UK
| | - Benjamin M Skinner
- />Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Rebecca O’Connor
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Gothami Fonseka
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Niclas Backström
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Yoichi Matsuda
- />Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810 Japan
| | - Peter Houde
- />Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA
| | - Erich D Jarvis
- />Department of Neurobiology, Duke University Medical Center, Box 3209, Durham, NC 27710 USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9PS UK
| | - Denis M Larkin
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Darren K Griffin
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
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Fuma S, Watanabe Y, Kawaguchi I, Takata T, Kubota Y, Ban-Nai T, Yoshida S. Derivation of hazardous doses for amphibians acutely exposed to ionising radiation. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2012; 103:15-19. [PMID: 22036153 DOI: 10.1016/j.jenvrad.2011.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 09/05/2011] [Accepted: 09/05/2011] [Indexed: 05/31/2023]
Abstract
Derivation of effect benchmark values for each taxonomic group, which has been difficult due to lack of experimental effects data, is required for more adequate protection of the environment from ionising radiation. Estimation of effects doses from nuclear DNA mass and subsequent species sensitivity distribution (SSD) analysis were proposed as a method for such a derivation in acute irradiation situations for assumed nuclear accident scenarios. As a case study, 5% hazardous doses (HD₅s), at which only 5% of species are acutely affected at 50% or higher lethality, were estimated on a global scale. After nuclear DNA mass data were obtained from a database, 50% lethal doses (LD₅₀s) for 4.8 and 36% of the global Anura and Caudata species, respectively, were estimated by correlative equations between nuclear DNA mass and LD₅₀s. Differences between estimated and experimental LD₅₀s were within a factor of three. The HD₅s obtained by the SSD analysis of these estimated LD₅₀s data were 5.0 and 3.1 Gy for Anura and Caudata, respectively. This approach was also applied to the derivation of regional HD₅s. The respective HD₅s were 6.5 and 3.2 Gy for Anura and Caudata inhabiting Japan. This HD₅ value for the Japanese Anura was significantly higher than the global value, while Caudata had no significant difference in global and Japanese HD₅s. These results suggest that this approach is also useful for derivation of regional benchmark values, some of which are likely different from the global values.
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Affiliation(s)
- Shoichi Fuma
- Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan.
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Nie H, Crooijmans RPMA, Bastiaansen JWM, Megens HJ, Groenen MAM. Regional regulation of transcription in the chicken genome. BMC Genomics 2010; 11:28. [PMID: 20074332 PMCID: PMC2817690 DOI: 10.1186/1471-2164-11-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 01/14/2010] [Indexed: 12/02/2022] Open
Abstract
Background Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis. Results We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes. Conclusions Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution. The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108
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Affiliation(s)
- Haisheng Nie
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands
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Jömann N, Clemen G, Greven H. Notes on cranial ontogeny and delayed metamorphosis in the hynobiid salamander Ranodon sibiricus Kessler, 1866 (Urodela). Ann Anat 2005; 187:305-21. [PMID: 16130831 DOI: 10.1016/j.aanat.2005.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The skull of larvae, juveniles and adults of the rare and primitive hynobiid salamander Ranodon sibiricus was re-examined using transparencies and illustrated by new graphics. The earliest larva available for investigations already had the dominant bones. The maxillary, however, was still lacking. Previous descriptions regarding the appearance and growth of bones could be largely confirmed. The vomer, first seen as a relatively small obliquely arranged dentate bar in the 3.8 cm long larva, became larger during ontogeny, but did not change its position remarkably. The vomerine pars dentalis with only a single tooth line was straight in larvae and juveniles, but was slightly curved in adults allowing for distinction of an outer and inner portion. This feature is typical and more pronounced in most other hynobiids. The significance of the vomer and vomerine dentition for systematic and phylogenetic purposes and its changes during metamorphosis are briefly discussed. Two of the specimens examined showed delayed metamorphosis very likely caused by low temperatures. Here the temporal course of transformation was "stretched" and therefore some alterations, e.g. regression of the palatinal portion of the palatopterygoid, were shown more clearly. Continuous growth of some skull elements in these individuals suggested a relative independence from metamorphosis perhaps due to variable thyroid activity and/or independent changes in individual tissue sensitivities. It is suggested that remodelling of the mouth roof could be used for staging urodele ontogeny.
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Affiliation(s)
- Norbert Jömann
- Institut für Evolution und Okologie der Tiere der Universität Münster, Hüfferstrasse 1, D-48149 Münster, Germany
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Ikebe C, Gu H, Ruan R, Kohno SI. Chromosomes of Hynobius chinensis Günther and Hynobius amjiensis Gu from China, and Comparison with Those of 19 Other Hynobius Species. Zoolog Sci 1998. [DOI: 10.2108/zsj.15.981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Iizuka K, Yazawa S. The karyotype, C-bands and AgNO3-bands of a lungless salamander from Korea:Onychodactylus fischeri (Boulenger) (Amphibia, Urodela). Cell Mol Life Sci 1994. [DOI: 10.1007/bf01984959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Iizuka K, Kezer J, Seto T. Karyotypes of two rare species of hynobiid salamanders from Taiwan, Hynobius sonani (Maki) and Hynobius formosanus Maki (Urodela). Genetica 1988. [DOI: 10.1007/bf00058841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cytogenetics of the chinese giant salamander, Andrias davidianus (Blanchard): the evolutionary significance of cryptobranchoid karyotypes. Chromosoma 1982. [DOI: 10.1007/bf00292262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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