DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species.
Citizen Science
Euborellia annulipes
Forficula auricularia
Nanopore sequencing
Journal
Biological research
ISSN: 0717-6287
Titre abrégé: Biol Res
Pays: England
ID NLM: 9308271
Informations de publication
Date de publication:
17 Feb 2023
17 Feb 2023
Historique:
received:
11
09
2022
accepted:
16
01
2023
entrez:
17
2
2023
pubmed:
18
2
2023
medline:
22
2
2023
Statut:
epublish
Résumé
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.
Sections du résumé
BACKGROUND
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
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
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.
Identifiants
pubmed: 36797803
doi: 10.1186/s40659-023-00414-9
pii: 10.1186/s40659-023-00414-9
pmc: PMC9935246
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6Subventions
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : Beca Magíster Nacional 22200502
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : MILENIO - ICN2021_044
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : CONICYT - FONDECYT 11160777
Investigateurs
Alan Phillips
(A)
Alejandro Aros
(A)
Alexandra Alarcón
(A)
Alonso Mendiboure
(A)
Alyson Sepúlveda
(A)
Amalia Zepeda
(A)
Angela Bustamante
(A)
Angelo Russu
(A)
Anselmo Martínez
(A)
Antonia Inostroza
(A)
Antonio Palma
(A)
Bárbara Ponce
(B)
Belén Báez
(B)
Belén Dianta
(B)
Benjamín Zenteno
(B)
Berenice Jelvez
(B)
Brisa Henríquez
(B)
Camila Concha
(C)
Catalina Fuentes
(C)
Catalina Morales
(C)
Claudia Inostrosa
(C)
Claudio Valenzuela
(C)
Constanza Dercolto
(C)
Cristian Malebrán
(C)
Damián González
(D)
Daniel Venegas
(D)
Dayhanne Alvear
(D)
Deyna Martínez
(D)
Diana Silva
(D)
Diego Abarca
(D)
Elías Fuentes
(E)
Elizabeth Inzunza
(E)
Fabián Alfaro
(F)
Fernanda Aqueveque
(F)
Fernanda Cartes
(F)
Fernanda Delgado
(F)
Fernanda Sandoval
(F)
Fernanda Tamayo
(F)
Francisco Espinoza
(F)
Gladys Espinoza
(G)
Gonzalo Inzunza
(G)
Gonzalo Vidal
(G)
Grisel Roca
(G)
Hileinn Sánchez
(H)
Jared Defaur
(J)
Jonathan Sazo
(J)
José Manuel Fuentes
(JM)
José Miguel Cañete
(JM)
Juan Pablo Vásquez
(JP)
Karin Reyes
(K)
Karina Piña
(K)
Katherien Orellana
(K)
Lisandro Vega
(L)
Loreto Lagos
(L)
Magdalena Ponce
(M)
Catalina Maldonado
(C)
María Alejandra González
(MA)
María Ignacia Torres
(MI)
Mariana Irribarra
(M)
Mariangela Sanguinetti
(M)
Mario Leiva
(M)
Marjorie Ibacache
(M)
Martín Yañez
(M)
Martina Palamara
(M)
Massimo Magnani
(M)
Maykol Padilla
(M)
Millaray Arancibia
(M)
Milovan Acevedo
(M)
Génesis Morales
(G)
Nallely Castillo
(N)
Nélida Carvajal
(N)
Omar González
(O)
Paola Alvarado
(P)
Pía Muñoz
(P)
Renata Erazo
(R)
Rocío Silva
(R)
Rodrigo Sepúlveda
(R)
Rodrigo Valdés
(R)
Ronny Molina
(R)
Saraí Costa
(S)
Sebastián Alvear
(S)
Sofía Acuña
(S)
Sofía Mendoza
(S)
Sofia Sáez
(S)
Sofía Tapia
(S)
Tamara Cerda
(T)
Tomás Zamorano
(T)
Valentina Araya
(V)
Valentina Cortez
(V)
Valentina Pereira
(V)
Valentina Pino
(V)
Victoria Yáñez
(V)
Viviana Jaramillo
(V)
Yavanna Rivera
(Y)
Yerko Urbina
(Y)
Zuleimy Uzcátegui
(Z)
Informations de copyright
© 2023. The Author(s).
Références
Sci Rep. 2021 May 13;11(1):10313
pubmed: 33986401
J Exp Zool B Mol Dev Evol. 2023 Jan;340(1):18-33
pubmed: 35167178
Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3024-3029
pubmed: 30642969
Gigascience. 2018 Apr 1;7(4):
pubmed: 29617771
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Ecol Evol. 2017 Jun 22;7(15):5939-5947
pubmed: 28811889
Genes (Basel). 2019 Nov 07;10(11):
pubmed: 31703372
Proc Natl Acad Sci U S A. 2017 May 2;114(18):4721-4726
pubmed: 28416702
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Emerg Infect Dis. 2016 Feb;22(2):331-4
pubmed: 26812583
Heredity (Edinb). 2000 Nov;85 Pt 5:444-9
pubmed: 11122422
Arthropod Struct Dev. 2010 Sep;39(5):360-8
pubmed: 20566316
Nucleic Acids Res. 2016 Jan 4;44(D1):D184-9
pubmed: 26673694
BMC Evol Biol. 2010 Nov 10;10:344
pubmed: 21062504
PLoS One. 2013 Jun 24;8(6):e66900
pubmed: 23826171
Science. 2011 Mar 18;331(6023):1386
pubmed: 21415334
Methods Mol Biol. 2019;1962:1-14
pubmed: 31020551
Nat Ecol Evol. 2018 Mar;2(3):557-566
pubmed: 29403074
Elife. 2016 Apr 07;5:
pubmed: 27054412
Arthropod Struct Dev. 2008 Jul;37(4):310-20
pubmed: 18396462
Results Probl Cell Differ. 2017;61:211-228
pubmed: 28409306
Insect Mol Biol. 2019 Dec;28(6):739-758
pubmed: 31120160
Nucleic Acids Res. 2022 Jan 7;50(D1):D1040-D1045
pubmed: 34792158
Annu Rev Entomol. 2021 Jan 7;66:355-372
pubmed: 32931312
Science. 2014 Nov 7;346(6210):763-7
pubmed: 25378627
G3 (Bethesda). 2020 Apr 9;10(4):1193-1196
pubmed: 32041730
Pest Manag Sci. 2021 Jan;77(1):159-167
pubmed: 33411365
Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457
pubmed: 32300014
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
PLoS One. 2011;6(7):e21800
pubmed: 21789182
Arthropod Struct Dev. 2000 Apr;29(2):137-46
pubmed: 18088922
Mol Phylogenet Evol. 2016 Jul;100:382-390
pubmed: 27033951
Methods Mol Biol. 2019;1962:227-245
pubmed: 31020564
Sci Rep. 2017 Dec 21;7(1):18022
pubmed: 29269933
Bioinformatics. 2018 Aug 1;34(15):2666-2669
pubmed: 29547981
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
PLoS One. 2014 Apr 10;9(4):e94098
pubmed: 24722757
J Biomol Tech. 2017 Apr;28(1):2-7
pubmed: 28337073
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Nucleic Acids Res. 2015 Jan;43(Database issue):D714-9
pubmed: 25332403
Bioinformatics. 2008 Jul 15;24(14):1650-1
pubmed: 18511468
PLoS Comput Biol. 2020 Jan 23;16(1):e1007314
pubmed: 31971941
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):
pubmed: 35042800
Proc Biol Sci. 2021 May 12;288(1950):20210150
pubmed: 33947234
Zootaxa. 2013;3703:1-82
pubmed: 26146682
Bioinformatics. 2016 Mar 1;32(5):767-9
pubmed: 26559507
Curr Protoc Bioinformatics. 2018 Jun;62(1):e51
pubmed: 29927072
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Biology (Basel). 2022 May 25;11(6):
pubmed: 35741328
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122
pubmed: 28460117
Annu Rev Entomol. 2018 Jan 7;63:31-45
pubmed: 28938083
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610