LTR retrotransposons from the Citrus x clementina genome: characterization and application
LTR retrotransposons from the Citrus x clementina genome: characterization and application
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DOI：
10.1007/s11295-018-1257-x
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发表时间：
2018-08-01
影响因子：
2.4
通讯作者：
Gmitter, Fred G., Jr.
中科院分区：
文献类型：
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作者：
Du, Dongliang;Du, Xiaoyun;Gmitter, Fred G., Jr.
长末端重复反转录转座子（LTR-RTs）是植物基因组的重要组成部分，是一种功能强大的分子标记系统。自2011年以来，第一个柑橘参考基因组（柑橘x小柑橘）已公开;然而，柑橘的先前研究尚未利用全基因组进行LTR-RT标记开发。在这项研究中，在C. X克莱门蒂娜基因组使用基于结构的（LTR_FINDER）和基于同源性的（RepeatMasker）方法。LTR-RTs首先根据蛋白质结构域分为Gypsy和Copia超家族，然后根据LTR序列相似性聚类为1074个家族。350个科皮亚家族被分为四个谱系：Retrofit、Tork、Sire和Oryco。178个吉普赛家庭被分为六个世系：Athila、达特、Renia、CRM、Galadriel和Del。大部分LTR-RT（3218或81.3%）锚定在9个Clementine柑橘连锁群，占目前组装的染色体的9.74%。采用17个反转录转座子间扩增多态性（IRAP）标记对25个芸香科物种进行基因分型。利用序列特异性扩增多态性（SSAP）标记对甜橙品种“瓦伦西亚”和“菠萝”进行了区分。x sinensis）和24个甜橙子无性系。从克莱门汀基因组开发的LTR-RT标记可以在芸香科中转移，证明它们是柑橘和芸香科遗传分析的极好工具。
Long terminal repeat retrotransposons (LTR-RTs) are a large portion of most plant genomes, and can be used as a powerful molecular marker system. The first citrus reference genome (Citrus x clementina) has been publicly available since 2011; however, previous studies in citrus have not utilized the whole genome for LTR-RT marker development. In this study, 3959 full-length LTR-RTs were identified in the C. x clementina genome using structure-based (LTR_FINDER) and homology-based (RepeatMasker) methods. LTR-RTs were first classified by protein domain into Gypsy and Copia superfamilies, and then clustered into 1074 families based on LTR sequence similarity. Three hundred fifty Copia families were grouped into four lineages: Retrofit, Tork, Sire, and Oryco. One hundred seventy-eight Gypsy families were sorted into six lineages: Athila, Tat, Renia, CRM, Galadriel, and Del. Most LTR-RTs (3218 or 81.3%) were anchored to the nine Clementine mandarin linkage groups, accounting for 9.74% of chromosomes currently assembled. Accessions of 25 Rutaceae species were genotyped using 17 inter-retrotransposon amplified polymorphism (IRAP) markers developed from conserved LTR regions. Sequence-specific amplified polymorphism (SSAP) makers were used to distinguish 'Valencia' and 'Pineapple' sweet oranges (C. x sinensis), and 24 sweet orange clones. LTR-RT markers developed from the Clementine genome can be transferred within the Rutaceae family demonstrating that they are an excellent tool for citrus and Rutaceae genetic analysis.