1
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Lim I, Park YJ, Ha J. Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies. Sci Rep 2024; 14:5226. [PMID: 38433262 PMCID: PMC10909864 DOI: 10.1038/s41598-024-55581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.
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Affiliation(s)
- Insu Lim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Yong-Jin Park
- Department of Plant Sciences, Kongju National University, Yesan, 340-702, Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea.
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2
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de Oliveira TD, de Freitas TR. Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia). Genet Mol Biol 2024; 46:e20230180. [PMID: 38315881 PMCID: PMC10842476 DOI: 10.1590/1678-4685-gmb-2023-0180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Contrary to predictions from classical hybrid sterility models of chromosomal speciation, some organisms display high rates of karyotype variation. Ctenomys are the current mammals with the greatest interspecific and intraspecific chromosomal variation. A large number of species have been studied cytogenetically. The diploid numbers of chromosomes range from 2n = 10 to 2n = 70. Here, we analyzed karyotype evolution in Ctenomys using comparative phylogenetic methods. We found a strong phylogenetic signal with chromosome number. This refutes the chromosomal megaevolution model, which proposes the independent accumulation of multiple chromosomal rearrangements in each closely related species. We found that Brownian motion (BM) described the observed characteristic changes more thoroughly than the Ornstein-Uhlenbeck and Early-Burst models. This suggests that the evolution of chromosome numbers occurs by a random walk along phylogenetic clades. However, our data indicate that the BM model alone does not fully characterize the chromosomal evolution of Ctenomys.
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Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Thales R.O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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3
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Oliveira da Silva W, Rosa CC, Ferguson-Smith MA, O'Brien PCM, Saldanha J, Rossi RV, Pieczarka JC, Nagamachi CY. The emergence of a new sex-system (XX/XY 1Y 2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae). Sci Rep 2022; 12:8690. [PMID: 35610291 PMCID: PMC9130129 DOI: 10.1038/s41598-022-12706-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/11/2022] [Indexed: 11/15/2022] Open
Abstract
X-autosome translocation (XY1Y2) has been reported in distinct groups of vertebrates suggesting that the rise of a multiple sex system within a species may act as a reproductive barrier and lead to speciation. The viability of this system has been linked with repetitive sequences located between sex and autosomal portions of the translocation. Herein, we investigate Oecomys auyantepui, using chromosome banding and Fluorescence In Situ Hybridization with telomeric and Hylaeamys megacephalus whole-chromosome probes, and phylogenetic reconstruction using mtDNA and nuDNA sequences. We describe an amended karyotype for O. auyantepui (2n = 64♀65♂/FNa = 84) and report for the first time a multiple sex system (XX/XY1Y2) in Oryzomyini rodents. Molecular data recovered O. auyantepui as a monophyletic taxon with high support and cytogenetic data indicate that O. auyantepui may exist in two lineages recognized by distinct sex systems. The Neo-X exhibits repetitive sequences located between sex and autosomal portions, which would act as a boundary between these two segments. The G-banding comparisons of the Neo-X chromosomes of other Sigmodontinae taxa revealed a similar banding pattern, suggesting that the autosomal segment in the Neo-X can be shared among the Sigmodontinae lineages with a XY1Y2 sex system.
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Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Celina Coelho Rosa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Juliane Saldanha
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
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4
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Reid WR, Olson KE, Franz AWE. Current Effector and Gene-Drive Developments to Engineer Arbovirus-Resistant Aedes aegypti (Diptera: Culicidae) for a Sustainable Population Replacement Strategy in the Field. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1987-1996. [PMID: 33704462 PMCID: PMC8421695 DOI: 10.1093/jme/tjab030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 05/13/2023]
Abstract
Arthropod-borne viruses (arboviruses) such as dengue, Zika, and chikungunya viruses cause morbidity and mortality among human populations living in the tropical regions of the world. Conventional mosquito control efforts based on insecticide treatments and/or the use of bednets and window curtains are currently insufficient to reduce arbovirus prevalence in affected regions. Novel, genetic strategies that are being developed involve the genetic manipulation of mosquitoes for population reduction and population replacement purposes. Population replacement aims at replacing arbovirus-susceptible wild-type mosquitoes in a target region with those that carry a laboratory-engineered antiviral effector to interrupt arboviral transmission in the field. The strategy has been primarily developed for Aedes aegypti (L.), the most important urban arbovirus vector. Antiviral effectors based on long dsRNAs, miRNAs, or ribozymes destroy viral RNA genomes and need to be linked to a robust gene drive to ensure their fixation in the target population. Synthetic gene-drive concepts are based on toxin/antidote, genetic incompatibility, and selfish genetic element principles. The CRISPR/Cas9 gene editing system can be configurated as a homing endonuclease gene (HEG) and HEG-based drives became the preferred choice for mosquitoes. HEGs are highly allele and nucleotide sequence-specific and therefore sensitive to single-nucleotide polymorphisms/resistant allele formation. Current research efforts test new HEG-based gene-drive designs that promise to be less sensitive to resistant allele formation. Safety aspects in conjunction with gene drives are being addressed by developing procedures that would allow a recall or overwriting of gene-drive transgenes once they have been released.
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Affiliation(s)
- William R Reid
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Ken E Olson
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Alexander W E Franz
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
- Corresponding author, e-mail:
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5
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Lucek K, Butlin RK, Patsiou T. Secondary contact zones of closely-related Erebia butterflies overlap with narrow phenotypic and parasitic clines. J Evol Biol 2020; 33:1152-1163. [PMID: 32573833 DOI: 10.1111/jeb.13669] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Zones of secondary contact between closely related taxa are a common legacy of the Quaternary ice ages. Despite their abundance, the factors that keep species apart and prevent hybridization are often unknown. Here, we study a very narrow contact zone between three closely related butterfly species of the Erebia tyndarus species complex. Using genomic data, we first determined whether gene flow occurs and then assessed whether it might be hampered by differences in chromosome number between some species. We found interspecific gene flow between sibling species that differ in karyotype by one chromosome. Conversely, only F1 hybrids occurred between two species that have the same karyotype, forming a steep genomic cline. In a second step, we fitted clines to phenotypic, ecological and parasitic data to identify the factors associated with the genetic cline. We found clines for phenotypic data and the prevalence of the endosymbiont parasite Wolbachia to overlap with the genetic cline, suggesting that they might be drivers for separating the two species. Overall, our results highlight that some gene flow is possible between closely related species despite different chromosome numbers, but that other barriers restrict such gene flow.
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Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Theofania Patsiou
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Institute of Plant Sciences, Department of Biology, University of Bern, Bern, Switzerland
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6
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Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A, Sanyal K. Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLife 2020; 9:e58556. [PMID: 32469306 PMCID: PMC7292649 DOI: 10.7554/elife.58556] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Centromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.
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Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Radha Mishra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | | | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Caoimhe E O'Brien
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Geraldine Butler
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
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7
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Comparative Tyramide-FISH mapping of the genes controlling flavor and bulb color in Allium species revealed an altered gene order. Sci Rep 2019; 9:12007. [PMID: 31427665 PMCID: PMC6700127 DOI: 10.1038/s41598-019-48564-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/07/2019] [Indexed: 01/29/2023] Open
Abstract
Evolutionarily related species often share a common order of genes along homeologous chromosomes. Here we report the collinearity disruption of genes located on homeologous chromosome 4 in Allium species. Ultra-sensitive fluorescence in situ hybridization with tyramide signal amplification (tyr-FISH) allowed the visualization of the alliinase multigene family, chalcon synthase gene and EST markers on Allium cepa and Allium fistulosum chromosomes. In A. cepa, bulb alliinase, root alliinase (ALL1) and chalcon synthase (CHS-B) genes were located in the long arm but EST markers (API18 and ACM082) were located in the short arm. In A. fistulosum, all the visualized genes and markers were located in the short arm. Moreover, root alliinase genes (ALL1 and AOB249) showed contrast patterns in number of loci. We suppose that the altered order of the genes/markers is the result of a large pericentric inversion. To get insight into the evolution of the chromosome rearrangement, we mapped the bulb alliinase gene in phylogenetically close and distant species. In the taxonomic clade including A. fistulosum, A. altaicum, A. oschaninii and A. pskemense and in phylogenetically distant species A. roylei and A. nutans, the bulb alliinase gene was located on the short arm of chromosome 4 while, in A. cepa and A. schoenoprasum, the bulb alliinase gene was located on the long arm of chromosome 4. These results have encouraging implications for the further tracing of inverted regions in meiosis of interspecific hybrids and studding chromosome evolution. Also, this finding may have a practical benefit as closely related species are actively used for improving onion crop stock.
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8
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Cserkész T, Rusin M, Sramkó G. An integrative systematic revision of the European southern birch mice (Rodentia: Sminthidae, S
icista subtilis
group). Mamm Rev 2015. [DOI: 10.1111/mam.12058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Tamás Cserkész
- Department of Systematic Zoology and Ecology; Eötvös Loránd University; Pázmány Péter sétány 1/c. H-1117 Budapest Hungary
| | - Mikhail Rusin
- Department of Evolutional and Genetical Systematics; Schmalhausen Institute of Zoology; Vul. B. Khmelnytskogo 15. 01601 Kiev Ukraine
| | - Gábor Sramkó
- Department of Botany; University of Debrecen; Egyetem tér 1. H-4032 Debrecen Hungary
- MTA-ELTE-MTM Ecology Research Group; Pázmány Péter sétány 1/c. H-1117 Budapest Hungary
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9
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Berríos S, Manieu C, López-Fenner J, Ayarza E, Page J, González M, Manterola M, Fernández-Donoso R. Robertsonian chromosomes and the nuclear architecture of mouse meiotic prophase spermatocytes. Biol Res 2014; 47:16. [PMID: 25027603 PMCID: PMC4101721 DOI: 10.1186/0717-6287-47-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 11/06/2022] Open
Abstract
Background The nuclear architecture of meiotic prophase spermatocytes is based on higher-order patterns of spatial associations among chromosomal domains from different bivalents. The meiotic nuclear architecture depends on the chromosome characteristics and consequently is prone to modification by chromosomal rearrangements. In this work, we consider Mus domesticus spermatocytes with diploid chromosome number 2n = 40, all telocentric, and investigate a possible modification of the ancestral nuclear architecture due to the emergence of derived Rb chromosomes, which may be present in the homozygous or heterozygous condition. Results In the 2n = 40 spermatocyte nuclei random associations mediated by pericentromeric heterochromatin among the 19 telocentric bivalents ocurr at the nuclear periphery. The observed frequency of associations among them, made distinguishable by specific probes and FISH, seems to be the same for pairs that may or may not form Rb chromosomes. In the homozygote Rb 2n = 24 spermatocytes, associations also mediated by pericentromeric heterochromatin occur mainly between the three telocentric or the eight metacentric bivalents themselves. In heterozygote Rb 2n = 32 spermatocytes all heterochromatin is localized at the nuclear periphery, yet associations are mainly observed among the three telocentric bivalents and between the asynaptic axes of the trivalents. Conclusions The Rb chromosomes pose sharp restrictions for interactions in the 2n = 24 and 2n = 32 spermatocytes, as compared to the ample possibilities for interactions between bivalents in the 2n = 40 spermatocytes. Undoubtedly the emergence of Rb chromosomes changes the ancestral nuclear architecture of 2n = 40 spermatocytes since they establish new types of interactions among chromosomal domains, particularly through centromeric and heterochromatic regions at the nuclear periphery among telocentric and at the nuclear center among Rb metacentric ones.
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10
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Huang C, Yu W, Xu Z, Qiu Y, Chen M, Qiu B, Motokawa M, Harada M, Li Y, Wu Y. A cryptic species of the Tylonycteris pachypus complex (Chiroptera: Vespertilionidae) and its population genetic structure in southern China and nearby regions. Int J Biol Sci 2014; 10:200-11. [PMID: 24550688 PMCID: PMC3927132 DOI: 10.7150/ijbs.7301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/09/2014] [Indexed: 11/08/2022] Open
Abstract
Three distinct bamboo bat species (Tylonycteris) are known to inhabit tropical and subtropical areas of Asia, i.e., T. pachypus, T. robustula, and T. pygmaeus. This study performed karyotypic examinations of 4 specimens from southern Chinese T. p. fulvidus populations and one specimen from Thai T. p. fulvidus population, which detected distinct karyotypes (2n=30) compared with previous karyotypic descriptions of T. p. pachypus (2n=46) and T. robustula (2n=32) from Malaysia. This finding suggested a cryptic Tylonycteris species within T. pachypus complex in China and Thailand. Morphometric studies indicated the difficulty in distinguishing the cryptic species and T. p. pachypus from Indonesia apart from the external measurements, which might be the reason for their historical misidentification. Based on 623 bp mtDNA COI segments, a phylogeographic examination including T. pachypus individuals from China and nearby regions, i.e., Vietnam, Laos, and Cambodia, was conducted to examine the population genetic structure. Genealogical and phylogeographical results indicated that at least two diverged lineages existed in these regions (average 3.4 % of Kimura 2-parameter distances) and their population structure did not match the geographic pattern. These results suggested that at least two historical colonizations have occurred by the cryptic species. Furthermore, through integration of traditional and geometric morphological results, morphological differences on zygomatic arches, toothrows and bullae were detected between two lineages in China. Given the similarity of vegetation and climate of Guangdong and Guangxi regions, we suggested that such differences might be derived from their historical adaptation or distinct evolutionary history rather than the differences of habitats they occurred currently.
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Affiliation(s)
- Chujing Huang
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Wenhua Yu
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhongxian Xu
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yuanxiong Qiu
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Miao Chen
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Bing Qiu
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | | | - Masashi Harada
- 3. Laboratory Animal Center, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Yuchun Li
- 4. Marine College, Shandong University (Weihai), Weihai 264209, China
| | - Yi Wu
- 1. College of Life Sciences, Guangzhou University, Guangzhou 510006, China
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11
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Palaeoploidization and adaptation: An evolutionary strategy among pteridophytes with a reference to Ophioglossum L. THE NUCLEUS 2013. [DOI: 10.1007/s13237-013-0085-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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12
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López‐López A, Hudson P, Galián J. Recent origin of a chiasmatic sex trivalent in
A
ustralian
P
seudotetracha
tiger beetles. J Zool (1987) 2012. [DOI: 10.1111/jzo.12003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A. López‐López
- Departamento de Zoología y Antropología Física Edificio Facultad de Veterinaria Universidad de Murcia Murcia Spain
| | - P. Hudson
- South Australian Museum Adelaide SA Australia
| | - J. Galián
- Departamento de Zoología y Antropología Física Edificio Facultad de Veterinaria Universidad de Murcia Murcia Spain
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13
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Isakova GK. Spontaneous mutagenesis as a possible causal factor for the origin of obligate embryonic diapause in mammals (a hypothesis). ACTA ACUST UNITED AC 2012. [DOI: 10.1134/s207905971206007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Hellborg L, Piškur J. Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis. EUKARYOTIC CELL 2009; 8:1739-49. [PMID: 19717738 PMCID: PMC2772400 DOI: 10.1128/ec.00115-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 08/24/2009] [Indexed: 11/20/2022]
Abstract
When the genome organizations of 30 native isolates belonging to a wine spoilage yeast, Dekkera (Brettanomyces) bruxellensis, a distant relative of Saccharomyces cerevisiae, were examined, the numbers of chromosomes varied drastically, from 4 to at least 9. When single gene probes were used in Southern analysis, the corresponding genes usually mapped to at least two chromosomal bands, excluding a simple haploid organization of the genome. When different loci were sequenced, in most cases, several different haplotypes were obtained for each single isolate, and they belonged to two subtypes. Phylogenetic reconstruction using haplotypes revealed that the sequences from different isolates belonging to one subtype were more similar to each other than to the sequences belonging to the other subtype within the isolate. Reanalysis of the genome sequence also confirmed that partially sequenced strain Y879 is not a simple haploid and that its genome contains approximately 1% polymorphic sites. The present situation could be explained by (i) a hybridization event where two similar but different genomes have recently fused together or (ii) an event where the diploid progenitor of all analyzed strains lost a regular sexual cycle, and the genome started to accumulate mutations.
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Affiliation(s)
- Linda Hellborg
- Department of Cell and Organism Biology, Lund University, Lund SE-223 62, Sweden
| | - Jure Piškur
- Department of Cell and Organism Biology, Lund University, Lund SE-223 62, Sweden
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15
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Ozery-Flato M, Shamir R. Sorting genomes with centromeres by translocations. J Comput Biol 2008; 15:793-812. [PMID: 18652529 DOI: 10.1089/cmb.2007.0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A centromere is a special region in the chromosome that plays a vital role during cell division. Every new chromosome created by a genome rearrangement event must have a centromere in order to survive. This constraint has been ignored in the computational modeling and analysis of genome rearrangements to date. Unlike genes, the different centromeres are indistinguishable, they have no orientation, and only their location is known. A prevalent rearrangement event in the evolution of multi-chromosomal species is translocation (i.e., the exchange of tails between two chromosomes). A translocation may create a chromosome with no centromere in it. In this paper, we study for the first time centromeres-aware genome rearrangements. We present a polynomial time algorithm for computing a shortest sequence of translocations transforming one genome into the other, where all of the intermediate chromosomes must contain centromeres. We view this as a first step towards analysis of more general genome rearrangement models that take centromeres into consideration.
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16
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Jolly CJ. A proper study for mankind: Analogies from the Papionin monkeys and their implications for human evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; Suppl 33:177-204. [PMID: 11786995 DOI: 10.1002/ajpa.10021] [Citation(s) in RCA: 192] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper's theme is that analogies drawn from the cercopithecine tribe Papionini, especially the African subtribe Papionina (baboons, mangabeys, and mandrills), can be a valuable source of insights about the evolution of the human tribe, Hominini, to complement homologies found in extant humans and/or African apes. Analogies, involving a "likeness of relations" of the form "A is to B, as X is to Y," can be usefully derived from nonhomologous (homoplastic) resemblances in morphology, behavior, ecology, or population structure. Pragmatically, the papionins are a fruitful source of analogies for hominins because they are phylogenetically close enough to share many basic attributes by homology, yet far enough that homoplastic modifications of these features are easily recognized as such. In "The Seedeaters," an analogy between Theropithecus among baboons and Australopithecus africanus among hominines was the source of a widely discussed (and often misrepresented) diet-based scenario of hominin origins that explained previously unassociated hominin apomorphies, interpreted basal hominins as nonhuman rather than prehuman primates, and accommodated a basal hominin adaptive radiation of at least two lines. Current usage recognizes an even more extensive evolutionary radiation among the basal hominins, originating no earlier than about 7 ma, with multiple lineages documented or inferred by 2.5 ma. Although multilineage clades (especially the Paranthropus clade) within this complex are widely recognized, and emerge from sophisticated, parsimony-based analyses, it is suspected that in many cases, developmental or functional homoplasies are overwhelming the phylogenetic signal in the data. The papionin analogy (specifically the splitting of the traditional, morphology-based genera Cercocebus and Papio mandated by molecular evidence) illustrates the power of these factors to produce erroneous cladograms. Moreover, the rapid deployment of basal hominins across varied African habitats was an ideal scenario for producing morphologically undetectable homoplasy. There seems to be no foolproof way to distinguish, a priori, homologous from homoplastic resemblances in morphology, but one pragmatic strategy is to severely censor the datset, retaining only resemblances or differences (often apparently trivial ones) that cannot be reasonably explained on the basis of functional resemblance or difference, respectively. This strategy may eliminate most morpological data, and leave many fossil taxa incertae sedis, but this is preferable to unwarranted phylogenetic confidence. Another source of phylogenetic uncertainty is the possibility of gene-flow by occasional hybridization between hominins belonging to ecologically and adaptively distinct species or even genera. Although the evidence is unsatisfactorily sparse, it suggests that among catarrhines generally, regardless of major chromosomal rearrangements, intersterility is roughly proportional to time since cladogenetic separation. On a papionin analogy, especially the crossability of Papio hamadryas with Macaca mulatta and Theropithecus gelada, crossing between extant hominine genera is unlikely to produce viable and fertile offspring, but any hominine species whose ancestries diverged less than 4 ma previously may well have been able to produce hybrid offspring that could, by backcrossing, introduce alien genes with the potential of spreading if advantageous. Selection against maladaptive traits would maintain adaptive complexes against occasional genetic infiltration, and the latter does not justify reducing the hybridizing forms to a conspecific or congeneric rank. Whether reticulation could explain apparent parallels in hominin dentition and brain size is uncertain, pending genetic investigation of these apparently complex traits. Widespread papionin taxa (such as Papio baboons and species-groups of the genus Macaca), like many such organisms, are distributed as a "patchwork" of nonoverlapping but often parapatric forms (allotaxa). Morphologically diagnosable, yet not reproductively isolated, most allotaxa would be designated species by the phylogenetic species concept, but subspecies by the biological species concept, and use of the term "allotaxa" avoids this inconsistency. A line of contact between allotaxa typically coincides with an ecotone, with neighboring allotaxa occupying similar econiches in slightly different habitats, and often exhibiting subtle, adaptive, morphological differences as well as their defining differences of pelage. "Hybrid zones," with a wide variety of internal genetic structures and dynamics, typically separate parapatric allotaxa. Current models attribute the formation and maintenance of allotaxa to rapid pulses of population expansion and contraction to and from refugia, driven by late Neogene climatic fluctuations. An overall similarity in depth of genetic diversity suggests that papionin taxa such as Papio baboons, rather than extant humans, may present the better analogy for human population structure of the "prereplacement" era. Neandertals and Afro-Arabian "premodern" populations may have been analogous to extant baboon (and macaque) allotaxa: "phylogenetic" species, but "biological" subspecies. "Replacement," in Europe, probably involved a rapidly sweeping hybrid zone, driven by differential population pressure from the "modern" side. Since the genetic outcome of hybridization at allotaxon boundaries is so variable, the problem of whether any Neandertal genes survived the sweep, and subsequent genetic upheavals, is a purely empirical one; if any genes passed "upstream" across the moving zone, they are likely to be those conferring local adaptive advantage, and markers linked to these. In general, extant papionin analogies suggest that the dynamics and interrelationships among hominin populations now known only from fossils are likely to have been more complex than we are likely to be able to discern from the evidence available, and also more complex than can be easily expressed in conventional taxonomic terminology.
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Affiliation(s)
- C J Jolly
- Department of Anthropology, New York University, New York, New York 10003, USA
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BRAHIM IKHYARHOUMOULD, CHATTI NOUREDDINE, BRITTON-DAVIDIAN JANICE, SAÏD KHALED. Origin and evolution of the Robertsonian populations of the house mouse (Rodentia, Muridae) in Tunisia based on allozyme studies. Biol J Linn Soc Lond 2005. [DOI: 10.1111/j.1095-8312.2005.00452.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bonnet-Garnier A, Claro F, Thévenon S, Gautier M, Hayes H. Identification by R-banding and FISH of chromosome arms involved in Robertsonian translocations in several deer species. Chromosome Res 2004; 11:649-63. [PMID: 14606627 DOI: 10.1023/a:1025981508867] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We constructed and analyzed the RBG-banded karyotype of five deer species: Chital (Axis axis), White-lipped deer (Cervus albirostris), Rusa deer (Cervus timorensis russa), Sambar deer (Cervus unicolor) and Eld's deer (Cervus eldi siamensis). Among these five species, only Eld's deer had been previously karyotyped using R-banding. In order to identify all the chromosome correspondences with cattle and precisely which chromosome arms are involved in Robertsonian translocations, we compared the karyotypes of these five species with those of the closely related and well-characterized species, cattle (Bos taurus) and Vietnamese Sika deer (Cervus nippon pseudaxis). Among these six deer species (the five above plus the Vietnamese Sika deer), we found thirteen different Robertsonian translocations involving nineteen different chromosome arms. Thirteen chromosome arms were identified by comparison of R-banding patterns only and the remaining six were either confirmed or identified by FISH-mapping of bovine or caprine probes previously localized in cattle. Finally, we observed that five of the thirteen Robertsonian translocations are shared by at least two species and that some chromosome arms are more frequently involved in Robertsonian translocations than others.
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Affiliation(s)
- A Bonnet-Garnier
- FRE2584-CNRS Instabilité du génome et cancer, Pavilion Trouillet-Rossignol, 26 rue d'Ulm, 75248 Paris cedex 05, France.
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Richard F, Messaoudi C, Bonnet-Garnier A, Lombard M, Dutrillaux B. Highly conserved chromosomes in an Asian squirrel (Menetes berdmorei, Rodentia: Sciuridae) as demonstrated by ZOO-FISH with human probes. Chromosome Res 2004; 11:597-603. [PMID: 14516068 DOI: 10.1023/a:1024905018685] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The chromosomes of Menetes berdmorei (Rodentia, Sciuridae, Sciurinae) were studied by ZOO-FISH using whole human chromosome probes. All homoeologies between M. berdmorei and human chromosomes were determined, except for two small chromosome segments. Twelve human chromosomes are conserved in a unique block of synteny; ten are split into two and one into three blocks. Thus, a small number of interchromosomal rearrangements, about twenty, separates human from this squirrel karyotype. Homoeologies between human and the presumed ancestral chromosomes of Sciurinae could also be deduced, as well as those with the presumed ancestral chromosomes of eutherian mammals. Sciurinae chromosomes appear to be much closer to those of non-rodent mammals than those of Muridae and Cricetidae species studied so far. Thus, they provide an interesting tool to link the rodent genome to those of other mammals.
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Affiliation(s)
- F Richard
- UMR 147 CNRS, Institut Curie, Section Recherche, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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Rumpler Y. Complementary approaches of cytogenetics and molecular biology to the taxonomy and study of speciation processes in lemurs. Evol Anthropol 2004. [DOI: 10.1002/evan.20010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ranganath HA, Aruna S. Hybridization, transgressive segregation and evolution of new genetic systems inDrosophila. J Genet 2003; 82:163-77. [PMID: 15133193 DOI: 10.1007/bf02715816] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Introgressive hybridization facilitates incorporation of genes from one species into the gene pool of another. Studies on long-term effects of introgressive hybridization in animal systems are sparse. Drosophila nasuta (2n = 8) and D. albomicans (2n = 6)-a pair of allopatric, morphologically almost identical, cross-fertile members of the nasuta subgroup of the immigrans species group-constitute an excellent system to analyse the impact of hybridization followed by transgressive segregation of parental characters in the hybrid progeny. Hybrid populations of D. nasuta and D. albomicans maintained for over 500 generations in the laboratory constitute new recombinant hybrid genomes, here termed cytoraces. The impact of hybridization, followed by introgression and transgressive segregation, on chromosomal constitution and karyotypes, some fitness parameters, isozymes, components of mating behaviour and mating preference reveals a complex pattern of interracial divergence among parental species and cytoraces. This assemblage of characters in different combinations in a laboratory hybrid zone allows us to study the emergence of new genetic systems. Here, we summarize results from our ongoing studies comparing these hybrid cytoraces with the parental species, and discuss the implications of these findings for our understanding of the evolution of new genetic systems.
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Affiliation(s)
- H A Ranganath
- Drosophila Stock Centre, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore 570 006, India.
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Rumpler Y, Hauwy M, Rabarivola C, Rakotoarisoa G, Dutrillaux B. Chromosomal evolution of the Hapalemur griseus subspecies (Malagasy Prosimian), including a new chromosomal polymorphic cytotype. Chromosome Res 2003; 10:145-53. [PMID: 11993935 DOI: 10.1023/a:1014953202718] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A cytogenetic study has been performed on Hapalemur griseus caught in different locations of the eastern and northern forests of Madagascar. This allowed the determination of the more precise distribution areas of the different subspecies and the isolation of a new cytogenetic polymorphic subspecies of H. griseus. The chromosomal changes distinguishing the different subspecies are Robertsonian translocations and gain of heterochromatin. The phylogeny established on chromosome comparison is compatible with the geographic distribution of the subspecies.
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Affiliation(s)
- Yves Rumpler
- ULP, Faculté de Médecine, Institut d'Embryologie, Strasbourg, France
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Noor MA, Grams KL, Bertucci LA, Reiland J. Chromosomal inversions and the reproductive isolation of species. Proc Natl Acad Sci U S A 2001; 98:12084-8. [PMID: 11593019 PMCID: PMC59771 DOI: 10.1073/pnas.221274498] [Citation(s) in RCA: 651] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2001] [Indexed: 11/18/2022] Open
Abstract
Recent genetic studies have suggested that many genes contribute to differences between closely related species that prevent gene exchange, particularly hybrid male sterility and female species preferences. We have examined the genetic basis of hybrid sterility and female species preferences in Drosophila pseudoobscura and Drosophila persimilis, two occasionally hybridizing North American species. Contrary to findings in other species groups, very few regions of the genome were associated with these characters, and these regions are associated also with fixed arrangement differences (inversions) between these species. From our results, we propose a preliminary genic model whereby inversions may contribute to the speciation process, thereby explaining the abundance of arrangement differences between closely related species that co-occur geographically. We suggest that inversions create linkage groups that cause sterility to persist between hybridizing taxa. The maintenance of this sterility allows the species to persist in the face of gene flow longer than without such inversions, and natural selection will have a greater opportunity to decrease the frequency of interspecies matings.
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Affiliation(s)
- M A Noor
- Department of Biological Sciences, Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
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Abstract
Several authors have proposed that speciation frequently occurs when a population becomes fixed for one or more chromosomal rearrangements that reduce fitness when they are heterozygous. This hypothesis has little theoretical support because mutations that cause a large reduction in fitness can be fixed through drift only in small, inbred populations. Moreover, the effects of chromosomal rearrangements on fitness are unpredictable and vary significantly between plants and animals. I argue that rearrangements reduce gene flow more by suppressing recombination and extending the effects of linked isolation genes than by reducing fitness. This unorthodox perspective has significant implications for speciation models and for the outcomes of contact between neospecies and their progenitor(s).
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Piálek J, Hauffe HC, Rodríguez-Clark KM, Searle JB. Raciation and speciation in house mice from the Alps: the role of chromosomes. Mol Ecol 2001; 10:613-25. [PMID: 11298973 DOI: 10.1046/j.1365-294x.2001.01209.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There are at least 24 different karyotypic races of house mouse in the central Alps, each characterized by a different complement of ancestral acrocentric and derived metacentric chromosomes; altogether 55 different metacentric chromosomes have been described from the region. We argue that this chromosome variation largely arose in situ. If these races were to make contact, in most cases they would produce F1 hybrids with substantial infertility (sometimes complete sterility), due to nondisjunction and germ cell death associated with the formation of long-chain and/or ring configurations at meiosis. We present fertility estimates to confirm this for two particular hybrid types, one of which demonstrates male-limited sterility (in accordance with Haldane's Rule). As well as a model for speciation in allopatry, the Alpine mouse populations are of interest with regards speciation in parapatry: we discuss a possible reinforcement event. Raciation of house mice appears to have happened on numerous occasions within the central Alps. To investigate one possible source of new karyotypic races, we use a two-dimensional stepping stone model to examine the generation of recombinant races within chromosomal hybrid zones. Using field-derived ecological data and laboratory-derived fertility estimates, we show that hybrid karyotypic races can be generated at a reasonable frequency in simulations. Our model complements others developed for flowering plants that also emphasize the potential of chromosomal hybrid zones in generating new stable karyotypic forms.
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Affiliation(s)
- J Piálek
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, CZ-675 02 Studenec 122, Czech Republic
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Rogatcheva MB, Ono T, Sonta S, Oda S, Borodin PM. Robertsonian metacentrics of the house musk shrew (Suncus murinus, Insectivora, Soricidae) lose the telomeric sequences in the centromeric area. Genes Genet Syst 2000; 75:155-8. [PMID: 10984840 DOI: 10.1266/ggs.75.155] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The house musk shrew, Suncus murinus, is polymorphic for five Robertsonian translocations (Rb8.17, 9.13, 10.12, 11.16, 14.15). Fluorescence in situ hybridisation with a biotin-labelled oligonucleotide, (TTAGGG)7, was performed to localise the telomeric DNA sequences at Rb chromosomes of heterozygous shrews. Hybridisation signals were observed at both ends of all chromosomes, but not at the pericentromeric areas of any of the Robertsonian metacentrics. Our results indicate a complete loss of the telomeric sequences at the fusion points of the Rb metacentrics in S. murinus.
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Affiliation(s)
- M B Rogatcheva
- Institute of Cytology and Genetics, Novosibirsk, Russia.
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Molecular Cell Biology: Role of Repetitive DNA in Nuclear Architecture and Chromosome Structure. ACTA ACUST UNITED AC 2000. [DOI: 10.1007/978-3-642-57203-6_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
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Affiliation(s)
- G R Wiens
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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