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特定的长末端重复序列反转录转座子在野生向日葵和栽培向日葵之间呈现拷贝数变异。

Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers.

作者信息

Mascagni Flavia, Vangelisti Alberto, Giordani Tommaso, Cavallini Andrea, Natali Lucia

机构信息

Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.

出版信息

Genes (Basel). 2018 Aug 29;9(9):433. doi: 10.3390/genes9090433.

DOI:10.3390/genes9090433
PMID:30158460
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6162735/
Abstract

The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower ( L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses.

摘要

基因组重复元件的变异与植物物种驯化之间的关系尚未完全明晰。在之前的研究中，通过Illumina DNA测序对向日葵（L.）长末端重复序列（LTR）反转录转座子的丰度及其与基因的距离变化进行了研究，以比较栽培品种和野生种质。在本研究中，我们注释并鉴定了22个特定的反转录转座子家族，其丰度在驯化型和野生型基因型之间存在差异。这些家族大多属于吉普赛超家族的染色病毒谱系，分布于所有染色体。我们还分析了它们与基因的距离。靠近反转录转座子的基因根据生化途径进行分类，并展示了驯化型和野生型基因型之间的差异。这些数据表明，与反转录转座子相关的结构变异可能已经发生，从而在野生型和驯化型基因型之间产生表型变异，这可能是通过影响那些靠近插入或缺失的反转录转座子且属于特定生化途径（如参与植物应激反应的途径）的基因的表达来实现的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/8980a697b131/genes-09-00433-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/593d550d68fd/genes-09-00433-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/c91c91884681/genes-09-00433-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/1b977084c338/genes-09-00433-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/fac13dc7f8a9/genes-09-00433-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/8980a697b131/genes-09-00433-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/593d550d68fd/genes-09-00433-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/c91c91884681/genes-09-00433-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/1b977084c338/genes-09-00433-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/fac13dc7f8a9/genes-09-00433-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/805c/6162735/8980a697b131/genes-09-00433-g005.jpg

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