TY - JOUR
T1 - DNA sequencing in the classroom
T2 - complete genome sequence of two earwig (Dermaptera; Insecta) species
AU - School Earwig Genome Consortium
AU - Kobayashi, Sanae
AU - Maldonado, Jonathan E.
AU - Gaete, Alexis
AU - Araya, Ingrid
AU - Aguado-Norese, Constanza
AU - Cumplido, Nicolás
AU - Díaz, Sebastián
AU - Espinoza, Alonso
AU - Fernández, Edelmira
AU - Gajardo, Felipe
AU - González-Ordenes, Felipe
AU - Hauyon, Khantati
AU - Maldonado, Piedad
AU - Maldonado, Rodrigo
AU - Pochet, Isabel
AU - Riveros, Aníbal
AU - Sandoval, Paula
AU - Sepúlveda-González, Ailynne
AU - Stuardo, Camila
AU - Tapia-Reyes, Patricio
AU - Thornton, Carolina
AU - Undurraga, Soledad
AU - Varas, Macarena
AU - Valdivieso, Camilo
AU - Phillips, Alan
AU - Aros, Alejandro
AU - Alarcón, Alexandra
AU - Mendiboure, Alonso
AU - Sepúlveda, Alyson
AU - Zepeda, Amalia
AU - Bustamante, Angela
AU - Russu, Angelo
AU - Martínez, Anselmo
AU - Inostroza, Antonia
AU - Palma, Antonio
AU - Ponce, Bárbara
AU - Báez, Belén
AU - Dianta, Belén
AU - Zenteno, Benjamín
AU - Jelvez, Berenice
AU - Henríquez, Brisa
AU - Concha, Camila
AU - Fuentes, Catalina
AU - Morales, Catalina
AU - Inostrosa, Claudia
AU - Valenzuela, Claudio
AU - Dercolto, Constanza
AU - Malebrán, Cristian
AU - Orellana, Ariel
AU - Montecino, Martín
N1 - © 2023. The Author(s).
PY - 2023/2/17
Y1 - 2023/2/17
N2 - Background: 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. Results: 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. Conclusions: 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.
AB - Background: 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. Results: 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. Conclusions: 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.
KW - Animals
KW - Chile
KW - Insecta/genetics
KW - Sequence Analysis, DNA
UR - http://www.scopus.com/inward/record.url?scp=85148257929&partnerID=8YFLogxK
U2 - 10.1186/s40659-023-00414-9
DO - 10.1186/s40659-023-00414-9
M3 - Article
C2 - 36797803
AN - SCOPUS:85148257929
SN - 0716-9760
VL - 56
SP - 6
JO - Biological Research
JF - Biological Research
IS - 1
M1 - 6
ER -