Progress in plant genome sequencing: Research directions

M. K. Bragina; D. A. Afonnikov; E. A. Salina

doi:10.18699/VJ19.459

Progress in plant genome sequencing: Research directions

Переведенное название: Прогресс в секвенировании геномов растений – направления исследований

M. K. Bragina, D. A. Afonnikov, E. A. Salina

Результат исследования: Научные публикации в периодических изданиях › статья › рецензирование

3 Цитирования (Scopus)

Аннотация

Геномные технологии претерпели значительные изменения с момента публикации первой последовательности генома растения Arabidopsis thaliana. Исследователи приняли на вооружение новые алгоритмы и технологии секвенирования и биоинформационные подходы для получения геномной последовательности, транскриптома и экзома для модельных и культурных видов растений, что позволило сделать глубокие выводы о биологии растений. В результате снижения затрат на секвенирование благодаря улучшению методов сборки и анализа геномов, количество и качество секвенированных геномов растений постоянно растет. В течение последних двадцати лет опубликовано более 300 геномных последовательностей растений. Хотя многие из опубликованных геномов считаются неполными, они, тем не менее, оказались ценным инструментом для идентификации генов-кандидатов, участвующих в формировании хозяйственно ценных признаков растений, для проведения работ по маркер-ориентированной и геномной селекции и сравнительного анализа геномов растений с целью установления основных закономерностей происхождения различных видов растений. В связи с тем, что высокого уровня покрытия и разрешения полногеномного секвенирования не хватает для обнаружения всех изменений в сложных образцах, стало развиваться целевое (таргетное) секвенирование, которое заключается в выделении и секвенировании определенной области генома. Основным преимуществом целевого секвенирования являются его высокая мощность обнаружения (способность идентифицировать новые варианты) и более высокое разрешение. Кроме того, активно развивается экзомное секвенирование (метод секвенирования только белок-кодирующих участков генов), позволяющее секвенировать участки генома, которые обогащены функциональными вариантами и демонстрируют низкий уровень содержания повторяющихся областей. В настоящем обзоре проведен анализ развития работ по секвенированию и построению «референсных» геномов растений. Сравниваются методы целевого секвенирования, базирующиеся на использовании референсной последовательности ДНК

Переведенное название	Прогресс в секвенировании геномов растений – направления исследований
Язык оригинала	английский
Страницы (с-по)	38-48
Число страниц	11
Журнал	Вавиловский журнал генетики и селекции
Том	23
Номер выпуска	1
DOI	https://doi.org/10.18699/VJ19.459
Состояние	Опубликовано - 1 янв. 2019

Ключевые слова

Exome sequencing
Genome
Plants
Sequencing approaches
Targeted sequencing

ГРНТИ

34 БИОЛОГИЯ

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10.18699/VJ19.459

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title = "Progress in plant genome sequencing: Research directions",

abstract = "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.",

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Progress in plant genome sequencing: Research directions. / Bragina, M. K.; Afonnikov, D. A.; Salina, E. A.

В: Вавиловский журнал генетики и селекции, Том 23, № 1, 01.01.2019, стр. 38-48.

Результат исследования: Научные публикации в периодических изданиях › статья › рецензирование

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AB - 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.

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KW - GENE

KW - EVOLUTION

KW - BARLEY

KW - MUTANT

KW - MAP

KW - MUTATIONS

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