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Unique sequence organization and small RNA expression of a "selfish" B chromosome. Chromosoma 2017; 126:753-768. [PMID: 28780664 DOI: 10.1007/s00412-017-0641-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 10/19/2022]
Abstract
B chromosomes are found in numerous plants and animals. These nonessential, supernumerary chromosomes are often composed primarily of noncoding DNA repeats similar to those found within transcriptionally "silenced" heterochromatin. In order to persist within their resident genomes, many B chromosomes exhibit exceptional cellular behaviors, including asymmetric segregation into gametes and induction of genome elimination during early development. An important goal in understanding these behaviors is to identify unique B chromosome sequences and characterize their transcriptional contributions. We investigated these properties by examining a paternally transmitted B chromosome known as paternal sex ratio (PSR), which is present in natural populations of the jewel wasp Nasonia vitripennis. To facilitate its own transmission, PSR severely biases the sex ratio by disrupting early chromatin remodeling processes. Through cytological mapping and other approaches, we identified multiple DNA repeats unique to PSR, as well as those found on the A chromosomes, suggesting that PSR arose through a merger of sequences from both within and outside the N. vitripennis genome. The majority of PSR-specific repeats are interspersed among each other across PSR's long arm, in contrast with the distinct "blocks" observed in other organisms' heterochromatin. Through transcriptional profiling, we identified a subset of repeat-associated, small RNAs expressed by PSR, most of which map to a single PSR-specific repeat. These RNAs are expressed at much higher levels than those arising from A chromosome-linked repeats, suggesting that in addition to its sequence organization, PSR's transcriptional properties differ substantially from the pericentromeric regions of the normal chromosomes.
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Li XY, Liu XL, Ding M, Li Z, Zhou L, Zhang XJ, Gui JF. A novel male-specific SET domain-containing gene setdm identified from extra microchromosomes of gibel carp males. Sci Bull (Beijing) 2017; 62:528-536. [PMID: 36659360 DOI: 10.1016/j.scib.2017.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/20/2017] [Accepted: 03/22/2017] [Indexed: 01/21/2023]
Abstract
Various genes have been screened on extra chromosomes, but their molecular characterization, expression pattern and biological function are still unclear. Here, we utilized a male-specific sequence of polyploid gibel carp (Carassius gibelio) to identify a novel male-specific SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain-containing gene setdm on extra microchromosomes of gibel carp males. And setdm was characterized in molecule and expression aspects, in which its expression was specific to testis, and had relative high transcription during middle/late stages of testis development. Moreover, prominent expression of Setdm in spermatogenic cells was observed in testis through immunofluorescence co-localization analysis. These results suggest that biological function of setdm might be related to testis development and spermatogenesis of gibel carp. Additionally, the homeologous gene setdmf of setdm, was also characterized, and its expression was gonad-specific, in which its expressed product was detected to mainly distribute in gametogenic cells of testis and ovary, and to have dynamic expression pattern similar to that of setdm. Based on the current results, we propose that the novel male-specific setdm on extra microchromosomes might be functional divergence gene of the gonad-specific setdmf. Therefore, these findings will help us to further understand evolutionary fate and functional role of genes on extra microchromosomes.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Li Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China.
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Navarro-Domínguez B, Ruiz-Ruano FJ, Cabrero J, Corral JM, López-León MD, Sharbel TF, Camacho JPM. Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. Sci Rep 2017; 7:45200. [PMID: 28367986 PMCID: PMC5377258 DOI: 10.1038/srep45200] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/22/2017] [Indexed: 01/20/2023] Open
Abstract
For many years, parasitic B chromosomes have been considered genetically inert elements. Here we show the presence of ten protein-coding genes in the B chromosome of the grasshopper Eyprepocnemis plorans. Four of these genes (CIP2A, GTPB6, KIF20A, and MTG1) were complete in the B chromosome whereas the six remaining (CKAP2, CAP-G, HYI, MYCB2, SLIT and TOP2A) were truncated. Five of these genes (CIP2A, CKAP2, CAP-G, KIF20A, and MYCB2) were significantly up-regulated in B-carrying individuals, as expected if they were actively transcribed from the B chromosome. This conclusion is supported by three truncated genes (CKAP2, CAP-G and MYCB2) which showed up-regulation only in the regions being present in the B chromosome. Our results indicate that B chromosomes are not so silenced as was hitherto believed. Interestingly, the five active genes in the B chromosome code for functions related with cell division, which is the main arena where B chromosome destiny is played. This suggests that B chromosome evolutionary success can lie on its gene content.
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Affiliation(s)
| | - Francisco J. Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - José María Corral
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
- Department of Bioanalytics, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | | | - Timothy F. Sharbel
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
- Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 4J8, Canada
| | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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Ma W, Gabriel TS, Martis MM, Gursinsky T, Schubert V, Vrána J, Doležel J, Grundlach H, Altschmied L, Scholz U, Himmelbach A, Behrens SE, Banaei-Moghaddam AM, Houben A. Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog. THE NEW PHYTOLOGIST 2017; 213:916-928. [PMID: 27468091 DOI: 10.1111/nph.14110] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/18/2016] [Indexed: 05/21/2023]
Abstract
B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.
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Affiliation(s)
- Wei Ma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Tobias Sebastian Gabriel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Mihaela Maria Martis
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- National Bioinformatics Infrastructure Sweden, Department of Clinical and Experimental Medicine, Linköping University, SE-558185, Linköping, Sweden
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Heidrun Grundlach
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Ali Mohammad Banaei-Moghaddam
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, PO Box 13145-1384, Tehran, Iran
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
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Valente GT, Nakajima RT, Fantinatti BEA, Marques DF, Almeida RO, Simões RP, Martins C. B chromosomes: from cytogenetics to systems biology. Chromosoma 2016; 126:73-81. [PMID: 27558128 DOI: 10.1007/s00412-016-0613-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 01/01/2023]
Abstract
Though hundreds to thousands of reports have described the distribution of B chromosomes among diverse eukaryote groups, a comprehensive theory of their biological role has not yet clearly emerged. B chromosomes are classically understood as a sea of repetitive DNA sequences that are poor in genes and are maintained by a parasitic-drive mechanism during cell division. Recent developments in high-throughput DNA/RNA analyses have increased the resolution of B chromosome biology beyond those of classical and molecular cytogenetic methods; B chromosomes contain many transcriptionally active sequences, including genes, and can modulate the activity of autosomal genes. Furthermore, the most recent knowledge obtained from omics analyses, which is associated with a systemic view, has demonstrated that B chromosomes can influence cell biology in a complex way, possibly favoring their own maintenance and perpetuation.
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Affiliation(s)
- Guilherme T Valente
- Department of Bioprocess and Biotechnology, Agronomic Science School, UNESP - Sao Paulo State University, Botucatu, SP, 18610-307, Brazil
| | - Rafael T Nakajima
- Department of Morphology, Institute of Biosciences, UNESP - Sao Paulo State University, Sao Paulo, Botucatu, 18618-689, Brazil
| | - Bruno E A Fantinatti
- Department of Morphology, Institute of Biosciences, UNESP - Sao Paulo State University, Sao Paulo, Botucatu, 18618-689, Brazil
| | - Diego F Marques
- Department of Morphology, Institute of Biosciences, UNESP - Sao Paulo State University, Sao Paulo, Botucatu, 18618-689, Brazil
| | - Rodrigo O Almeida
- Department of Bioprocess and Biotechnology, Agronomic Science School, UNESP - Sao Paulo State University, Botucatu, SP, 18610-307, Brazil
| | - Rafael P Simões
- Department of Bioprocess and Biotechnology, Agronomic Science School, UNESP - Sao Paulo State University, Botucatu, SP, 18610-307, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, UNESP - Sao Paulo State University, Sao Paulo, Botucatu, 18618-689, Brazil.
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Fantinatti BEA, Martins C. Development of chromosomal markers based on next-generation sequencing: the B chromosome of the cichlid fish Astatotilapia latifasciata as a model. BMC Genet 2016; 17:119. [PMID: 27539214 PMCID: PMC4991083 DOI: 10.1186/s12863-016-0427-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/14/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND B chromosomes (Bs) are additional chromosomal elements found in a wide range of eukaryotes including fungi, plants and animals. B chromosomes are still enigmatic despite being the subject of hundreds, even thousands of reports. As yet there is no comprehensive theory for the biological role of B chromsomes thus, new studies are needed. Next-generation sequencing (NGS) holds promise for investigating classical issues in chromosome biology. NGS uses a large-scale approach that is required for advancing classical cytogenetic studies. Based on 454 sequencing data of a microdissected B chromosome and Illumina whole-genome sequencing data generated for 0B, 1B and 2B animals, we developed PCR- and qPCR-based markers for the B chromosomes of the cichlid fish Astatotilapia latifasciata (that possess 0, 1 or 2 B chromosomes). RESULTS Specific PCR primers were designed to produce two amplified fragments for B-positive samples and the control fragment for B-negative samples. Thus, PCR markers detected the presence/absence of Bs but did not provide information about the number of Bs. However, quantitative PCR (qPCR) markers clearly discriminated between 1B and 2B samples. The high copy number of the marker identified in the B chromosomes was confirmed by chromosome mapping. CONCLUSIONS The analysis of chromosome polymorphisms based on a NGS approach is a powerful strategy to obtain markers that detect the presence/absence of extra chromosomes or the gain or loss of genomic blocks. Further, qPCR can also provide information regarding the relative copy number of specific DNA fragments. These methods are useful to investigate various chromosome polymorphisms, including B and sex chromosomes, as well as chromosomal duplications and deletions. NGS data provide a detailed analysis of the composition of genomic regions that are thought to be present in B chromosomes.
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Affiliation(s)
- Bruno E A Fantinatti
- Departamento de Morfologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, CEP 18618-689, Botucatu, SP, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, CEP 18618-689, Botucatu, SP, Brazil.
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