通过基于标签化测序的转录组文库测序选择用于泛基因组研究的亚麻基因型。

Selection of Flax Genotypes for Pan-Genomic Studies by Sequencing Tagmentation-Based Transcriptome Libraries.

作者信息

Pushkova Elena N, Borkhert Elena V, Novakovskiy Roman O, Dvorianinova Ekaterina M, Rozhmina Tatiana A, Zhuchenko Alexander A, Zhernova Daiana A, Turba Anastasia A, Yablokov Arthur G, Sigova Elizaveta A, Krasnov George S, Bolsheva Nadezhda L, Melnikova Nataliya V, Dmitriev Alexey A

机构信息

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.

Moscow Institute of Physics and Technology, 141701 Moscow, Russia.

出版信息

Plants (Basel). 2023 Oct 30;12(21):3725. doi: 10.3390/plants12213725.

DOI:10.3390/plants12213725

PMID:37960081

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10650069/

Abstract

Flax ( L.) products are used in the food, pharmaceutical, textile, polymer, medical, and other industries. The creation of a pan-genome will be an important advance in flax research and breeding. The selection of flax genotypes that sufficiently cover the species diversity is a crucial step for the pan-genomic study. For this purpose, we have adapted a method based on Illumina sequencing of transcriptome libraries prepared using the Tn5 transposase (tagmentase). This approach reduces the cost of sample preparation compared to commercial kits and allows the generation of a large number of cDNA libraries in a short time. RNA-seq data were obtained for 192 flax plants (3-6 individual plants from 44 flax accessions of different morphology and geographical origin). Evaluation of the genetic relationship between flax plants based on the sequencing data revealed incorrect species identification for five accessions. Therefore, these accessions were excluded from the sample set for the pan-genomic study. For the remaining samples, typical genotypes were selected to provide the most comprehensive genetic diversity of flax for pan-genome construction. Thus, high-throughput sequencing of tagmentation-based transcriptome libraries showed high efficiency in assessing the genetic relationship of flax samples and allowed us to select genotypes for the flax pan-genomic analysis.

摘要

亚麻（L.）产品应用于食品、制药、纺织、聚合物、医疗及其他行业。构建泛基因组将是亚麻研究与育种的一项重要进展。选择能充分涵盖物种多样性的亚麻基因型是泛基因组研究的关键步骤。为此，我们采用了一种基于使用Tn5转座酶（片段化酶）制备的转录组文库进行Illumina测序的方法。与商业试剂盒相比，这种方法降低了样品制备成本，并能在短时间内生成大量cDNA文库。我们获得了192株亚麻植株（来自44个不同形态和地理来源的亚麻种质，每个种质3 - 6株单株）的RNA-seq数据。基于测序数据对亚麻植株间遗传关系的评估显示，有五个种质的物种鉴定错误。因此，这些种质被排除在泛基因组研究样本集之外。对于其余样本，选择了典型基因型以提供用于构建泛基因组的最全面的亚麻遗传多样性。因此，基于片段化的转录组文库的高通量测序在评估亚麻样本的遗传关系方面显示出高效率，并使我们能够为亚麻泛基因组分析选择基因型。