Crop pangenomes
Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2021-03-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/2916 |
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| author | A. Yu. Pronozin M. K. Bragina E. A. Salina |
| author_facet | A. Yu. Pronozin M. K. Bragina E. A. Salina |
| author_sort | A. Yu. Pronozin |
| collection | DOAJ |
| description | Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specif ic for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described. |
| format | Article |
| id | doaj-art-2155d8d8c1f44552b15e21a6114e77be |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2021-03-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-2155d8d8c1f44552b15e21a6114e77be2025-02-01T09:58:09ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592021-03-01251576310.18699/VJ21.0071132Crop pangenomesA. Yu. Pronozin0M. K. Bragina1E. A. Salina2Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesProgress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specif ic for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described.https://vavilov.elpub.ru/jour/article/view/2916agricultural plantsgenomespangenomesgenesevolutionbioinformatics analysiscomputational pipelines |
| spellingShingle | A. Yu. Pronozin M. K. Bragina E. A. Salina Crop pangenomes Вавиловский журнал генетики и селекции agricultural plants genomes pangenomes genes evolution bioinformatics analysis computational pipelines |
| title | Crop pangenomes |
| title_full | Crop pangenomes |
| title_fullStr | Crop pangenomes |
| title_full_unstemmed | Crop pangenomes |
| title_short | Crop pangenomes |
| title_sort | crop pangenomes |
| topic | agricultural plants genomes pangenomes genes evolution bioinformatics analysis computational pipelines |
| url | https://vavilov.elpub.ru/jour/article/view/2916 |
| work_keys_str_mv | AT ayupronozin croppangenomes AT mkbragina croppangenomes AT easalina croppangenomes |