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Haenel Q, Laurentino TG, Roesti M, Berner D. Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics. Mol Ecol 2018; 27:2477-2497. [PMID: 29676042 DOI: 10.1111/mec.14699] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant and fungal species. Our quantitative analysis reveals a strong and taxonomically widespread reduction of the crossover rate in the centre of chromosomes relative to their peripheries. We demonstrate that this pattern is poorly explained by the position of the centromere, but find that the magnitude of the relative reduction in the crossover rate in chromosome centres increases with chromosome length. That is, long chromosomes often display a dramatically low crossover rate in their centre, whereas short chromosomes exhibit a relatively homogeneous crossover rate. This observation is compatible with a model in which crossover is initiated from the chromosome tips, an idea with preliminary support from mechanistic investigations of meiotic recombination. Consequently, we show that organisms achieve a higher genome-wide crossover rate by evolving smaller chromosomes. Summarizing theory and providing empirical examples, we finally highlight that taxonomically widespread and systematic heterogeneity in crossover rate along chromosomes generates predictable broad-scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome. We conclude by emphasizing that chromosome-scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns.
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Affiliation(s)
- Quiterie Haenel
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Marius Roesti
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
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Coelho LM, Cursino-Santos JR, Persinoti GF, Rossi A, Martinez-Rossi NM. The Microsporum canis genome is organized into five chromosomes based on evidence from electrophoretic karyotyping and chromosome end mapping. Med Mycol 2012; 51:208-13. [PMID: 22852750 DOI: 10.3109/13693786.2012.701338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The karyotype of Microsporum canis was analyzed by contoured-clamped homogeneous electric field (CHEF) gel electrophoresis. Four chromosomal bands that correspond to five chromosomes ranging from 3.0-6.2 Mb were identified, adding the total genome size to approximately 24.9 Mb. To confirm the number of chromosomes in M. canis, the number of telomeres was assessed by using a telomeric probe (TTAGGG)(4) in Southern blot analyses of digested genomic DNA. Treatment of M. canis DNA with Bal31 exonuclease revealed progressive shortening of the DNA fragments positive for the (TTAGGG)(4) sequence, supporting location of repeats at the chromosome ends. These results can aid in improving the understanding of the genetic characterization of M. canis and the molecular epidemiology of dermatophytoses caused by this fungus.
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Affiliation(s)
- Luciene M Coelho
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination. BMC Genomics 2007; 8:100. [PMID: 17428342 PMCID: PMC1871584 DOI: 10.1186/1471-2164-8-100] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2006] [Accepted: 04/11/2007] [Indexed: 11/18/2022] Open
Abstract
Background Conidia are considered to be the primary cause of infections by Trichophyton rubrum. Results We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles. By functional analysis, we provided a global view of an important biological system related to conidial germination, including characterization of the pattern of gene expression at sequential developmental phases, and changes of gene expression profiles corresponding to morphological transitions. We matched the EST sequences to GO terms in the Saccharomyces Genome Database (SGD). A number of homologues of Saccharomyces cerevisiae genes related to signalling pathways and some important cellular processes were found to be involved in T. rubrum germination. These genes and signalling pathways may play roles in distinct steps, such as activating conidial germination, maintenance of isotropic growth, establishment of cell polarity and morphological transitions. Conclusion Our results may provide insights into molecular mechanisms of conidial germination at the cell level, and may enhance our understanding of regulation of gene expression related to the morphological construction of T. rubrum.
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Wang L, Ma L, Leng W, Liu T, Yu L, Yang J, Yang L, Zhang W, Zhang Q, Dong J, Xue Y, Zhu Y, Xu X, Wan Z, Ding G, Yu F, Tu K, Li Y, Li R, Shen Y, Jin Q. Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags. BMC Genomics 2006; 7:255. [PMID: 17032460 PMCID: PMC1621083 DOI: 10.1186/1471-2164-7-255] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2006] [Accepted: 10/11/2006] [Indexed: 11/20/2022] Open
Abstract
Background Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a recognized pathogen for humans, little is known about how its transcriptional pattern is related to development of the fungus and establishment of disease. It is therefore necessary to identify genes whose expression is relevant to growth, metabolism and virulence of T. rubrum. Results We generated 10 cDNA libraries covering nearly the entire growth phase and used them to isolate 11,085 unique expressed sequence tags (ESTs), including 3,816 contigs and 7,269 singletons. Comparisons with the GenBank non-redundant (NR) protein database revealed putative functions or matched homologs from other organisms for 7,764 (70%) of the ESTs. The remaining 3,321 (30%) of ESTs were only weakly similar or not similar to known sequences, suggesting that these ESTs represent novel genes. Conclusion The present data provide a comprehensive view of fungal physiological processes including metabolism, sexual and asexual growth cycles, signal transduction and pathogenic mechanisms.
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Affiliation(s)
- Lingling Wang
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Li Ma
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Wenchuan Leng
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Tao Liu
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Lu Yu
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Jian Yang
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Li Yang
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Wenliang Zhang
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Qian Zhang
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Jie Dong
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Ying Xue
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Yafang Zhu
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Xingye Xu
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
| | - Zhe Wan
- Research Centre for Medical Mycology, Beijing 100034, China
| | - Guohui Ding
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fudong Yu
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kang Tu
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruoyu Li
- Research Centre for Medical Mycology, Beijing 100034, China
| | - Yan Shen
- Chinese National Human Genome Center, Beijing, Beijing 100176, China
| | - Qi Jin
- State Key Lab for Molecular Virology and Genetic Engineering, Beijing 100176, China
- The Institute of Pathogen Microbiology, Chinese Academy of Medical Science, Beijing 100730, China
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Lukácsi G, Takó M, Nyilasi I. Pulsed-field gel electrophoresis: a versatile tool for analysis of fungal genomes. A review. Acta Microbiol Immunol Hung 2006; 53:95-104. [PMID: 16696553 DOI: 10.1556/amicr.53.2006.1.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The separation of chromosome-size DNA molecules by pulsed-field gel electrophoresis (PFGE) has become a well-established technique in recent years. Although it has very wide-ranging applications, it made a real breakthrough for fungal genome analysis. Because of the small size of fungal chromosomes, their investigation was not possible earlier. Different PFGE approaches allowed the separation of DNA molecules larger than 10 megabase pairs in size, and electrophoretic karyotypes for numerous previously genetically uncharacterized fungal species could be established. This review discusses the applicability of these electrophoretic karyotypes for the investigation of genome structure, for strain identification and for species delimitation.
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Affiliation(s)
- Gyöngyi Lukácsi
- Department of Microbiology, Faculty of Sciences, University of Szeged, P.O. Box 533, H-6701 Szeged, Hungary.
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