Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid Triticum and Aegilops species
Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid Triticum and Aegilops species
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DOI：
10.1007/s10722-017-0567-4
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发表时间：
2018-03
影响因子：
2
通讯作者：
K. Yamane;T. Kawahara
中科院分区：
文献类型：
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作者：
K. Yamane;T. Kawahara
叶绿体简单重复序列（cpSSR）广泛存在于所有植物的叶绿体基因组中，常用于基因型和系统发育分析。然而，在cpSSR的物种内和物种间的变化的信息是缺乏的。本研究对小麦和山羊草属12个四倍体57份材料和4个六倍体16份材料的叶绿体基因间（非编码区）DNA序列进行了测定。这些序列数据添加到我们以前的数据二倍体物种在相同的叶绿体区域。分析了13个二倍体、12个四倍体和4个六倍体小黑麦和山羊草属物种的189份材料的种内和种间遗传变异，使所有物种都由多份材料代表。这些数据被用来推断小麦和山羊草种内的系统发育关系。基于这个强大的系统发育树，8个cpSSR位点中有7个明显表现出“大小同源性”，指的是即使等位基因不是来自共同祖先，也可以出现相同大小和DNA序列的cpSSR。这些数据表明，cpSSR在系统发育分析中应谨慎使用。有趣的是，从几个以前的研究中观察到，我们的数据还表明，观察到的突变率可能会显着增加时，monopoltide（均聚物）重复数达到或超过9 bp。利用该数据集，在189份材料中检测到81种独特的单倍型，并成功鉴定了5个四倍体小麦和山羊草属物种。我们的研究结果表明，叶绿体核苷酸序列的核苷酸取代，插入缺失和SSR的组合可用于在物种登录水平的基因分型。
Chloroplast simple sequence repeats (cpSSRs) are widely distributed in the chloroplast genomes of all plant species, and are frequently employed for genotypic and phylogenetic analysis. However, information on intra- and interspecies variation in cpSSRs is lacking. In this study, we sequenced four intergenic (non-coding) chloroplast DNA regions in 57 accessions of 12 tetraploid, and 16 accessions of 4 hexaploid species ofTriticumandAegilops. These sequence data added to our previous data for diploid species in the same chloroplast regions. Intra- and interspecific genetic variation was analyzed for a total of 189 accessions of 13 diploid, 12 tetraploid, and 4 hexaploid species ofTriticumandAegilops,such that all species were represented by multiple accessions. The data were used to infer phylogenetic relationships within and amongTriticumandAegilopsspecies. Based on this robust phylogenetic tree, seven of eight cpSSR loci clearly exhibited “size homoplasy,” referring to the fact that cpSSRs of identical size and DNA sequence can arise even if the alleles are not descended from a common ancestor. These data indicate that cpSSRs should be used with caution in phylogenetic analyzes. Interestingly, as observed from several previous studies, our data also suggest that observed mutation rates may increase significantly when mononucleotide (homopolymer) repeat numbers reach or exceed 9 bp. In the present report, using this sequence data set involving cpSSRs, 81 unique haplotypes among 189 accessions were detected, and five tetraploidTriticumandAegilopsspecies were successfully identified and genotyped. Our results indicate that combinations of nucleotide substitutions, indels and SSRs of chloroplast nucleotide sequences are available for genotyping at the species accession level.