Sicat Juan Paolo A, Visendi Paul, Sewe Steven O, Bouvaine Sophie, Seal Susan E
Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK.
Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
Mob DNA. 2022 Apr 19;13(1):12. doi: 10.1186/s13100-022-00270-6.
Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most damaging in terms of its broad crop host range and its ability to serve as vector for over 400 plant viruses. Genomes of whiteflies belonging to this species complex have provided valuable genomic data; however, transposable elements (TEs) within these genomes remain unexplored. This study provides the first accurate characterization of TE content within the B. tabaci species complex.
This study identified that an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. The majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content of the three whitefly genomes with three other hemipteran genomes and found significantly more DNA transposons and less LINEs in the whitefly genomes. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE). The sequences of the identified TEs were clustered which generated 5766 TE clusters. A total of 2707 clusters were identified as uniquely found within the whitefly genomes while none of the generated clusters were from both whitefly and non-whitefly TE sequences. This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes.
This study is the first to characterize the landscape of TEs within the B. tabaci whitefly species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy significant portions of B. tabaci genomes, with DNA transposons representing the vast majority. This study also identified TE superfamilies and clusters of TE sequences of potential interest, providing essential information, and a framework for future TE studies within this species complex.
粉虱是农业害虫，在全球范围内对作物产量造成负面影响，有时会导致严重的经济损失和粮食不安全。烟粉虱物种复合体就其广泛的作物寄主范围以及作为400多种植物病毒载体的能力而言，是最具破坏性的。属于该物种复合体的粉虱基因组已提供了有价值的基因组数据；然而，这些基因组中的转座元件（TEs）仍未得到探索。本研究首次对烟粉虱物种复合体内的TE含量进行了准确表征。
本研究确定，三种粉虱物种（MEAM1、MEDQ和SSA - ECA）基因组平均有40.61%由TEs组成。鉴定出的大多数TEs是DNA转座子（平均22.85%），而短散在核元件（SINEs，平均0.14%）占比最少。本研究还将三种粉虱基因组的TE含量与其他三种半翅目基因组进行了比较，发现粉虱基因组中的DNA转座子明显更多，而长散在核元件（LINEs）更少。共鉴定出63个TE超家族存在于三种粉虱物种中（39个DNA转座子、6个长末端重复序列（LTR）、16个LINE和2个SINE）。鉴定出的TEs序列被聚类，产生了5766个TE簇。共鉴定出2707个簇是粉虱基因组中独有的，而生成的簇中没有一个来自粉虱和非粉虱的TE序列。本研究首次对不同烟粉虱物种中发现的TEs进行了表征，并创建了一个标准化的注释工作流程，可用于分析未来的粉虱基因组。
本研究首次对烟粉虱物种复合体内的TE景观进行了表征。对三种粉虱基因组中这些元件的表征表明，TEs占据了烟粉虱基因组的很大一部分，其中DNA转座子占绝大多数。本研究还鉴定出了潜在感兴趣的TE超家族和TE序列簇，为该物种复合体内未来的TE研究提供了重要信息和框架。
