沙鞭转录组简单重复序列(SSR)位点特征分析

Characteristics Analysis of Simple Sequence Repeat(SSR)Loci in Psammochloa villosa(Poaceae)Based on Transcriptome Data

沙鞭是禾本科、沙鞭属的一种多年生大型根茎类草本植物,主要分布于青海柴达木盆地和内蒙古高原及其毗邻荒漠地区,具有较强的耐旱、耐寒、耐碱、抗风沙和抗病能力。本研究使用MISA(Microsatellite identification tool)软件对沙鞭全长转录组测序获得的184076条Unigenes的SSR位点进行搜索和特征分析,共获得3563个SSR重复序列,分布于56824条Unigenes上,SSR发生和出现频率分别为30.87%和50.83%;重复类型以单核苷酸、二核苷酸和三核苷酸重复为主。单核苷酸重复中,(A/T)_(n)基元类型占总SSR位点的42.26%;二核苷酸重复优势基元类型为(AG/CT)_(n),占总SSR位点的9.29%。SSR数量随重复次数增加而降低;重复次数类型随基元序列长度增长而减少。此外,本研究还得到沙鞭29444条和10864条Unigenes的KOG和GO注释,其主要集中于翻译后修饰、蛋白质周转、催化活性和代谢过程。因此,本研究认为沙鞭转录组SSR序列呈现较高的多态性潜能,具有较大的开发价值,为今后沙鞭分子标记开发、辅助育种、种质资源评价提供了理论依据。

Psammochloa villosa is a perennial herb with large rhizomes of Psammochloa in Poaceae,which is mainly distributed in the desert area of the Qaidam Basin in Qinghai Province,and the Inner Mongolia Plateau and its adjacent desert areas.It has strong resistantace to drought,cold,alkali,wind and sand,and disease resistance.In this study,we searched and characterized SSR sites of 184076 unigenes obtained through high-throughput sequencing of full-length transcriptoions of Psammochloa villosa with the microsatellite identification tool software.A total of 93563 SSR sequences were obtained,which were distributed in 56824 unigenes.The occurrence and appearance frequency of SSRs were 30.87%and 50.83%,respectively;and the dominant repeat motifs of SSRs within transcriptomes were mono-,di-and tri-nucleotide.During the mono-nucleotide repeat,the motif type of(A/T)_(n) accounted for 42.26%of the total SSR loci,whereas the dominant motif type of di-nucleotide repeats was(AG/CT)_(n),which was 9.29%of the total SSR loci.Meanwhile,the number of SSRs decreased with increasing of repetition number,while the type of repetition numbers basically decreased with increasing of the length of motif sequences.Additionally,we also obtained the KOG and GO functional annotations of 29444 and 10864 Unigenes,whose major functions were focused on post-translational modifications,protein turnover,catalytic activity,and metabolic processes.Thus,we thought that SSR sequences of the transcriptome of Psammochloa villosa showed higher polymorphism potential,which had greater developmental values.The study provided theoretical basis for the development of molecular markers,auxiliary breeding,and evaluation of germplasm resources of Psammochloa villosa.