Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes
Background: The number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity...
| Main Authors: | , , , , , , , , , |
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| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
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2017
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| Online Access: | http://hdl.handle.net/20.500.12123/1322 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1579-0 https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1579-0?site=bmcgenomics.biomedcentral.com https://doi.org/10.1186/s12864-015-1579-0 |
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| author | Garbus, Ingrid Romero, José Rodolfo Miroslav, Valarik Vanzurova, Hana Karafiatova, Miroslava Caccamo, Mario Dolezel, Jaroslav Tranquilli, Gabriela Helguera, Marcelo Echenique, Carmen Viviana |
| author_browse | Caccamo, Mario Dolezel, Jaroslav Echenique, Carmen Viviana Garbus, Ingrid Helguera, Marcelo Karafiatova, Miroslava Miroslav, Valarik Romero, José Rodolfo Tranquilli, Gabriela Vanzurova, Hana |
| author_facet | Garbus, Ingrid Romero, José Rodolfo Miroslav, Valarik Vanzurova, Hana Karafiatova, Miroslava Caccamo, Mario Dolezel, Jaroslav Tranquilli, Gabriela Helguera, Marcelo Echenique, Carmen Viviana |
| author_sort | Garbus, Ingrid |
| collection | INTA Digital |
| description | Background:
The number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity to study the repetitive portion of each chromosome, enabling comparisons among them. Additionally, different sequencing approaches may produce different depth of insight to repeatome content and structure. In this work we analyze and characterize the repetitive sequences of Triticum aestivum cv. Chinese Spring homeologous group 4 chromosome arms, obtained through Roche 454 and Illumina sequencing technologies, hereinafter marked by subscripts 454 and I, respectively. Repetitive sequences were identified with the RepeatMasker software using the interspersed repeat database mips-REdat_v9.0p. The input sequences consisted of our 4DS454 and 4DL454 scaffolds and 4ASI, 4ALI, 4BSI, 4BLI, 4DSI and 4DLI contigs, downloaded from the International Wheat Genome Sequencing Consortium (IWGSC).
Results: Repetitive sequences content varied from 55% to 63% for all chromosome arm assemblies except for 4DLI, in which the repeat content was 38%. Transposable elements, small RNA, satellites, simple repeats and low complexity sequences were analyzed. SSR frequency was found one per 24 to 27 kb for all chromosome assemblies except 4DLI, where it was three times higher. Dinucleotides and trinucleotides were the most abundant SSR repeat units. (GA)n/(TC)n was the most abundant SSR except for 4DLI where the most frequently identified SSR was (CCG/CGG)n. Retrotransposons followed by DNA transposons were the most highly represented sequence repeats, mainly composed of CACTA/En-Spm and Gypsy superfamilies, respectively. This whole chromosome sequence analysis allowed identification of three new LTR retrotransposon families belonging to the Copia superfamily, one belonging to the Gypsy superfamily and two TRIM retrotransposon families. Their physical distribution in wheat genome was analyzed by fluorescent in situ hybridization (FISH) and one of them, the Carmen retrotransposon, was found specific for centromeric regions of all wheat chromosomes.
Conclusion: The presented work is the first deep report of wheat repetitive sequences analyzed at the chromosome arm level, revealing the first insight into the repeatome of T. aestivum chromosomes of homeologous group 4. |
| format | info:ar-repo/semantics/artículo |
| id | INTA1322 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | INTA13222018-01-11T18:29:59Z Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes Garbus, Ingrid Romero, José Rodolfo Miroslav, Valarik Vanzurova, Hana Karafiatova, Miroslava Caccamo, Mario Dolezel, Jaroslav Tranquilli, Gabriela Helguera, Marcelo Echenique, Carmen Viviana Trigo Wheat Chromosomes Nucleotide Sequence Genetics DNA Triticum Aestivum Cromosomas Secuencia Nucleotídica Genética ADN Cromosoma HD Background: The number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity to study the repetitive portion of each chromosome, enabling comparisons among them. Additionally, different sequencing approaches may produce different depth of insight to repeatome content and structure. In this work we analyze and characterize the repetitive sequences of Triticum aestivum cv. Chinese Spring homeologous group 4 chromosome arms, obtained through Roche 454 and Illumina sequencing technologies, hereinafter marked by subscripts 454 and I, respectively. Repetitive sequences were identified with the RepeatMasker software using the interspersed repeat database mips-REdat_v9.0p. The input sequences consisted of our 4DS454 and 4DL454 scaffolds and 4ASI, 4ALI, 4BSI, 4BLI, 4DSI and 4DLI contigs, downloaded from the International Wheat Genome Sequencing Consortium (IWGSC). Results: Repetitive sequences content varied from 55% to 63% for all chromosome arm assemblies except for 4DLI, in which the repeat content was 38%. Transposable elements, small RNA, satellites, simple repeats and low complexity sequences were analyzed. SSR frequency was found one per 24 to 27 kb for all chromosome assemblies except 4DLI, where it was three times higher. Dinucleotides and trinucleotides were the most abundant SSR repeat units. (GA)n/(TC)n was the most abundant SSR except for 4DLI where the most frequently identified SSR was (CCG/CGG)n. Retrotransposons followed by DNA transposons were the most highly represented sequence repeats, mainly composed of CACTA/En-Spm and Gypsy superfamilies, respectively. This whole chromosome sequence analysis allowed identification of three new LTR retrotransposon families belonging to the Copia superfamily, one belonging to the Gypsy superfamily and two TRIM retrotransposon families. Their physical distribution in wheat genome was analyzed by fluorescent in situ hybridization (FISH) and one of them, the Carmen retrotransposon, was found specific for centromeric regions of all wheat chromosomes. Conclusion: The presented work is the first deep report of wheat repetitive sequences analyzed at the chromosome arm level, revealing the first insight into the repeatome of T. aestivum chromosomes of homeologous group 4. Fil: Garbus, Ingrid. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Conicet - Bahia Blanca. Centro Recursos Naturales Renovables de Zona Semiarida(i); Argentina Fil: Romero, José Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Conicet - Bahia Blanca. Centro Recursos Naturales Renovables de Zona Semiarida(i); Argentina Fil: Miroslav, Valarik. Centre of the Region Haná for Biotechnological and Agricultural Research. Institute of Experimental Botany; República Checa Fil: Vanzurova, Hana. Centre of the Region Haná for Biotechnological and Agricultural Research. Institute of Experimental Botany; República Checa Fil: Karafiatova, Miroslava. Centre of the Region Haná for Biotechnological and Agricultural Research. Institute of Experimental Botany; República Checa Fil: Caccamo, Mario. Norwich Research Park. Genome Analysis Centre; Reino Unido Fil: Dolezel, Jaroslav. Centre of the Region Haná for Biotechnological and Agricultural Research. Institute of Experimental Botany; República Checa Fil: Tranquilli, Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto Recursos Biológicos; Argentina Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; Argentina Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Conicet - Bahia Blanca. Centro Recursos Naturales Renovables de Zona Semiarida(i); Argentina 2017-09-26T15:57:20Z 2017-09-26T15:57:20Z 2015 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/1322 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1579-0 https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1579-0?site=bmcgenomics.biomedcentral.com 1471-2164 https://doi.org/10.1186/s12864-015-1579-0 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf BMC Genomics 16 (375) : 1-16. (2015) |
| spellingShingle | Trigo Wheat Chromosomes Nucleotide Sequence Genetics DNA Triticum Aestivum Cromosomas Secuencia Nucleotídica Genética ADN Cromosoma HD Garbus, Ingrid Romero, José Rodolfo Miroslav, Valarik Vanzurova, Hana Karafiatova, Miroslava Caccamo, Mario Dolezel, Jaroslav Tranquilli, Gabriela Helguera, Marcelo Echenique, Carmen Viviana Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes |
| title | Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes |
| title_full | Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes |
| title_fullStr | Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes |
| title_full_unstemmed | Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes |
| title_short | Characterization of the repetitive DNA landscape in wheat homeologous group 4 chromosomes |
| title_sort | characterization of the repetitive dna landscape in wheat homeologous group 4 chromosomes |
| topic | Trigo Wheat Chromosomes Nucleotide Sequence Genetics DNA Triticum Aestivum Cromosomas Secuencia Nucleotídica Genética ADN Cromosoma HD |
| url | http://hdl.handle.net/20.500.12123/1322 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1579-0 https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1579-0?site=bmcgenomics.biomedcentral.com https://doi.org/10.1186/s12864-015-1579-0 |
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