Millennium Institute Center for Genome Regulation, 7800003, Santiago, Chile.
Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile.
Biol Res. 2023 Feb 17;56(1):6. doi: 10.1186/s40659-023-00414-9.
Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools.
The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera.
This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.
尽管昆虫代表了动物生命中最大的一部分，但已测序的昆虫物种数量仅数百种。耳形目（耳虫）缺乏基因组信息，尽管它是最基础的昆虫群体之一，而且在农业生态系统中很重要。作为国家基因组教育和推广计划的一部分，制定了一项计划，让高中生参与基因组测序项目。智利 12 所学校的学生被指示在其地理区域捕获耳虫标本，对其进行识别，并提供材料，由他们自己在学校进行基因组测序。
学校学生采集了两种世界性耳虫物种的标本：Euborellia annulipes（Anisolabididae 科）和 Forficula auricularia（Forficulidae 科）。提取基因组 DNA，在前往学校的科学团队的帮助下，使用纳米孔测序仪进行测序。获得的两种物种的序列数据进行组装和注释。我们获得了 1.18Gb（F. auricularia）和 0.94Gb（E. annulipes）的基因组大小，预测的编码蛋白基因数量分别为 31800 和 40000。我们的分析表明，我们能够捕获高比例（≥93%）的保守蛋白，表明这些基因组可用于比较和功能分析。我们还能够表征重复序列和非编码 RNA 基因等结构元件。最后，每个物种中过度表达的基因功能类别表明，在生殖细胞形成和它们之间的繁殖方式背后存在重要差异，这些特征是区分这两个遥远的 Dermaptera 科的生物特性之一。
这项工作代表了科学界和普通社区前所未有地合作进行基因组测序项目的实例。纳米孔测序仪的多功能性和可及性是该计划成功的关键。我们能够获得以前未在这一水平上分析过的两种重要且广泛分布的昆虫的全基因组序列。该项目提供的数据应阐明未来对 Dermaptera 的研究。
