Haq Inzamam Ul, Muhammad Majid, Yuan Huang, Ali Shahbaz, Abbasi Asim, Asad Muhammad, Ashraf Hafiza Javaria, Khurshid Aroosa, Zhang Kexin, Zhang Qiangyan, Liu Changzhong
College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China.
College of Life Sciences, Shaanxi Normal University, Xi'an 710100, China.
Life (Basel). 2022 Mar 31;12(4):521. doi: 10.3390/life12040521.
(fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of , particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1-15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30-35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in account for a considerable proportion of the genome's repetitive fraction. The satellite DNA families' repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of .
草地贪夜蛾是夜蛾总科的成员，夜蛾总科占所有鳞翅目的三分之一以上，包括大量农业和森林害虫物种。草地贪夜蛾是一种多食性物种，是全球重要的农业害虫，凸显了其经济重要性。其基因组大小、组装、系统发育分类和转录组分析此前均有描述。然而，不同研究报告的占据整个组装基因组的重复DNA序列组成不同，且草地贪夜蛾基因组也缺乏对动态卫星DNA的全面研究。我们利用来自八个不同地理区域的公开可用原始基因组数据，对地理上相距遥远的草地贪夜蛾种群的重复DNA，特别是卫星DNA进行了比较分析。我们的结果表明，除了Maverick和PIF/Harbinger元件（其重复拷贝存在差异）外，大多数转座元件（TEs）在所有地理上相距遥远的样本中普遍存在。TEs年龄分析表明，大多数TEs家族由100万至1500万年的年轻拷贝组成；然而，PIF/Harbinger有一些3000万至3500万年的较老/退化拷贝。共发现了七个卫星DNA家族，约占草地贪夜蛾整个基因组的0.65%。卫星DNA家族的重复图谱分析揭示了不同的读取深度覆盖或拷贝数。卫星DNA家族的大小范围从最小的108 bp SfrSat06 - 108家族到最大的（1824 bp）SfrSat07 - 1824家族。我们没有观察到单体长度与每个卫星家族的K2P分歧、拷贝数或丰度之间存在统计学上的显著相关性。我们的研究结果表明，在草地贪夜蛾中鉴定出的卫星DNA家族占基因组重复部分的相当比例。卫星DNA家族的重复图谱显示沿参考序列存在点突变。在地理上相距遥远的草地贪夜蛾种群之间存在有限的TEs分化。
