Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, 36036-900, Brazil.
Embrapa Gado de Leite, Juiz de Fora, Minas Gerais, 36038-330, Brazil.
Mol Biol Rep. 2020 Jun;47(6):4911-4915. doi: 10.1007/s11033-020-05445-z. Epub 2020 Apr 23.
Microsatellite primers were developed in Lippia alba complex to better understanding the origins and evolution of the species. We sought to increase the numbers of available simple sequence repeat (SSR) markers. We performed low-coverage (~ twofold) genomic DNA sequencing of a diploid accession and generated a de novo assembly comprising 175,572 contigs. Sixteen SSR loci were selected and of these 13 SSR loci were successfully amplified in 20 L. alba tetraploid accessions and in 12 other Lippia species. Only one SSR locus was monomorphic, whereas 12 loci were polymorphic, yielding one to nine alleles. The heterozygosity was similar among markers, with values of 0.274-0.485; the polymorphism information content values varied from 0.237 to 0.367. These markers were successfully amplified in related species with 85% of transferability on average. Thus, we demonstrate the utility of including a de novo assembly step to obtain SSR markers from low-coverage genomic datasets.
为了更好地了解物种的起源和进化，我们在 Lippia alba 复合体中开发了微卫星引物。我们试图增加可用的简单重复序列（SSR）标记的数量。我们对一个二倍体品系进行了低覆盖率（~两倍）的基因组 DNA 测序，并生成了一个由 175572 个 contigs 组成的从头组装。选择了 16 个 SSR 位点，其中 13 个 SSR 位点在 20 个 L. alba 四倍体品系和 12 个其他 Lippia 种中成功扩增。只有一个 SSR 位点是单态的，而 12 个位点是多态的，产生了 1 到 9 个等位基因。标记之间的杂合度相似，值在 0.274-0.485 之间；多态信息含量值从 0.237 到 0.367 不等。这些标记在相关物种中平均有 85%的可转移性，因此，我们证明了在获得低覆盖率基因组数据集的 SSR 标记时，包括从头组装步骤的有效性。
