目标:硬粒小麦,普通小麦,和面包小麦,普通小麦,是最近起源的两种异源多倍体物种,它们在栽培的数千年中经历了严格的选择计划。在本文中,我们研究了硬粒小麦卫星,并与以前发表的面包小麦卫星进行了比较分析。
方法:我们使用satMiner方案揭示了硬粒小麦卫星组,该方案基于RepeatExplerr2对Illumina读数的连续聚类,并使用RepeatMaskerv4.0.5估计了每个鉴定的satDNA的丰度和变异。我们还进行了深satDNA家族表征,包括通过硬粒小麦的荧光原位杂交(FISH)进行的染色体定位,以及与面包小麦的FISH模式的比较。基本局部比对搜索工具(BLAST®)用于通过NCBI的基因组数据查看器(GDW)追踪硬粒小麦基因组组装中的每个satDNA,并比较了两个物种的基因组组装。使用MEGA11估算了硬粒和面包小麦的同源satDNA家族之间的序列差异和一致周转率(CTR)。
结果:这项研究表明,在非常短的时间内,两个物种的卫星DNA(satDNAs)集都发生了重大的定性和定量变化,随着重复数和每个卫星基因座的扩展/收缩,每个物种都不同,对于大多数这些卫星来说,序列的变化率很高,除了所分析的两个物种之间没有共享的satDNAs的出现/损失。这些satDNA的进化变化在物种之间很常见,但这项研究真正值得注意和新颖的是,这些过程发生在两个物种分离的不到8000年的时间里,表明它们的satdna加速进化。
结论:这些结果,以及许多这些卫星与转座因子的关系,以及它们在着丝粒和染色体亚端粒区水平上产生的多态性,在这些物种的进化起源以及人类在整个栽培历史中施加的选择压力的背景下进行了分析和讨论。
OBJECTIVE: Durum wheat, Triticum turgidum, and bread wheat, Triticum aestivum, are two allopolyploid species of very recent origin that have been subjected to intense selection programs during the thousands of years they have been cultivated. In this paper, we study the durum wheat satellitome and establish a comparative analysis with the previously published bread wheat satellitome.
METHODS: We revealed the durum wheat satellitome using the satMiner protocol which is based on consecutive rounds of clustering of Illumina reads by RepeatExplorer2, and estimated abundance and variation for each identified satDNA with RepeatMasker v4.0.5. We have also performed a deep satDNA families characterization including chromosomal location by Fluorescence In Situ Hybridization (FISH) in durum wheat and its comparison with FISH patterns in bread wheat. Basic Local Alignment Search Tool (BLAST®) was used for trailing each satDNA in the assembly of durum wheat genome through NCBI\'s Genome Data Viewer (GDW) and the genome assemblies of both species were compared. Sequence divergence and consensus turnover rate (CTR) between homologous satDNA families of durum and bread wheat were estimated using MEGA11.
RESULTS: This study reveals that in an exceedingly short period, significant qualitative and quantitative changes have occurred in the set of satellite DNAs (satDNAs) of both species, with expansions/contractions of the number of repeats and the loci per satellite, different in each species, and a high rate of sequence change for most of these satellites, in addition to the emergence/loss of satDNAs not shared between the two species analysed. These evolutionary changes in satDNA are common between species but what is truly remarkable and novel about this study is that these processes have taken place in less than the last ~8000 years separating the two species, indicating an accelerated evolution of their satDNAs.
CONCLUSIONS: These results, together with the relationship of many of these satellites with transposable elements and the polymorphisms they generate at the level of centromeres and subtelomeric regions of their chromosomes, are analysed and discussed in the context of the evolutionary origin of these species and the selection pressure exerted by man throughout the history of their cultivation.