Progress in plant genome sequencing: research directions
Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model an...
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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
2019-02-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/1866 |
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| author | M. K. Bragina D. A. Afonnikov E. A. Salina |
| author_facet | M. K. Bragina D. A. Afonnikov E. A. Salina |
| author_sort | M. K. Bragina |
| collection | DOAJ |
| description | Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished. |
| format | Article |
| id | doaj-art-9f3e6fa6ab6c4c39bb1d094d9bbe4f7e |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2019-02-01 |
| 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-9f3e6fa6ab6c4c39bb1d094d9bbe4f7e2025-02-01T09:58:07ZengSiberian 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 селекции2500-32592019-02-01231384810.18699/VJ19.459869Progress in plant genome sequencing: research directionsM. K. Bragina0D. A. Afonnikov1E. A. Salina2Institute of Cytology and Genetics, SB RASInstitute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics, SB RASSince the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.https://vavilov.elpub.ru/jour/article/view/1866plantssequencing approachesgenomeexome sequencingtargeted sequencing |
| spellingShingle | M. K. Bragina D. A. Afonnikov E. A. Salina Progress in plant genome sequencing: research directions Вавиловский журнал генетики и селекции plants sequencing approaches genome exome sequencing targeted sequencing |
| title | Progress in plant genome sequencing: research directions |
| title_full | Progress in plant genome sequencing: research directions |
| title_fullStr | Progress in plant genome sequencing: research directions |
| title_full_unstemmed | Progress in plant genome sequencing: research directions |
| title_short | Progress in plant genome sequencing: research directions |
| title_sort | progress in plant genome sequencing research directions |
| topic | plants sequencing approaches genome exome sequencing targeted sequencing |
| url | https://vavilov.elpub.ru/jour/article/view/1866 |
| work_keys_str_mv | AT mkbragina progressinplantgenomesequencingresearchdirections AT daafonnikov progressinplantgenomesequencingresearchdirections AT easalina progressinplantgenomesequencingresearchdirections |