Comparative Evolutionary Genomics in Insects

Barbara Feldmeyer; Erich Bornberg-Bauer; Elias Dohmen; Bertrand Fouks; Jacqueline Heckenhauer; Ann Kathrin Huylmans; Alun R. C. Jones; Eckart Stolle; Mark C. Harrison

doi:10.1007/978-1-0716-3838-5_16

Comparative Evolutionary Genomics in Insects

Barbara Feldmeyer, Erich Bornberg-Bauer, Elias Dohmen, Bertrand Fouks, Jacqueline Heckenhauer, Ann Kathrin Huylmans, Alun R. C. Jones, Eckart Stolle, Mark C. Harrison

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

1 Citation (Scopus)

Abstract

Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.

Original language	English
Title of host publication	Comparative Genomics
Subtitle of host publication	Methods and Protocols
Editors	João Carlos Setubal, Peter F. Stadler, Jens Stoye
Place of Publication	New York, NY
Publisher	Humana Press
Chapter	16
Pages	473-514
Number of pages	42
Edition	2
ISBN (Electronic)	978-1-0716-3838-5
ISBN (Print)	978-1-0716-3837-8, 978-1-0716-3840-8
DOIs	https://doi.org/10.1007/978-1-0716-3838-5_16
Publication status	Published - 1 Jun 2024
Externally published	Yes

Publication series

Name	Methods in Molecular Biology
Publisher	Springer
Volume	2802
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Funding

EBB, BaFe, ED, JH, AKH, ES, and MCH are members of the DFG funded priority program, Genomic Basis of Evolutionary Innovations (GEvol): SPP2349. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—project numbers: 502865717 (JH), 503307636 (AKH), 503307636 (BaFe), 433110898, 445756277, 503360601 (ES), 503348080 (ED, EBB), and 503320462 (MCH). ARCJ is funded by the HFSP grant RPG0060/2018 to EBB. BeFo is supported by an EU-H2020 MSCA-IF-2020 fellowship (101024100, TEEPI). Deutscher Akademischer Austauschdienst (DAAD)—project number 57598585 (ES).

Funders	Funder number
Deutsche Forschungsgemeinschaft	SPP2349, 502865717, 503307636, 433110898, 445756277, 503360601, 503348080, 503320462
Human Frontier Science Program	RPG0060/2018
European Horizon 2020	101024100
Deutscher Akademischer Austauschdienst	57598585

Access to Document

10.1007/978-1-0716-3838-5_16

Cite this

Feldmeyer, B., Bornberg-Bauer, E., Dohmen, E., Fouks, B., Heckenhauer, J., Huylmans, A. K., Jones, A. R. C., Stolle, E., & Harrison, M. C. (2024). Comparative Evolutionary Genomics in Insects. In J. C. Setubal, P. F. Stadler, & J. Stoye (Eds.), Comparative Genomics: Methods and Protocols (2 ed., pp. 473-514). (Methods in Molecular Biology; Vol. 2802). Humana Press. https://doi.org/10.1007/978-1-0716-3838-5_16

Comparative Evolutionary Genomics in Insects. / Feldmeyer, Barbara; Bornberg-Bauer, Erich; Dohmen, Elias et al.
Comparative Genomics: Methods and Protocols. ed. / João Carlos Setubal; Peter F. Stadler; Jens Stoye. 2. ed. New York, NY: Humana Press, 2024. p. 473-514 (Methods in Molecular Biology; Vol. 2802).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Feldmeyer, B, Bornberg-Bauer, E, Dohmen, E, Fouks, B, Heckenhauer, J, Huylmans, AK, Jones, ARC, Stolle, E & Harrison, MC 2024, Comparative Evolutionary Genomics in Insects. in JC Setubal, PF Stadler & J Stoye (eds), Comparative Genomics: Methods and Protocols. 2 edn, Methods in Molecular Biology, vol. 2802, Humana Press, New York, NY, pp. 473-514. https://doi.org/10.1007/978-1-0716-3838-5_16

@inbook{c4b4abc4ad26452bb95372adf2420574,

title = "Comparative Evolutionary Genomics in Insects",

abstract = "Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.",

author = "Barbara Feldmeyer and Erich Bornberg-Bauer and Elias Dohmen and Bertrand Fouks and Jacqueline Heckenhauer and Huylmans, {Ann Kathrin} and Jones, {Alun R. C.} and Eckart Stolle and Harrison, {Mark C.}",

year = "2024",

month = jun,

day = "1",

doi = "10.1007/978-1-0716-3838-5_16",

language = "English",

isbn = "978-1-0716-3837-8",

series = "Methods in Molecular Biology",

publisher = "Humana Press",

pages = "473--514",

editor = "Setubal, {Jo{\~a}o Carlos} and Stadler, {Peter F.} and Jens Stoye",

booktitle = "Comparative Genomics",

address = "United States",

edition = "2",

}

TY - CHAP

T1 - Comparative Evolutionary Genomics in Insects

AU - Feldmeyer, Barbara

AU - Bornberg-Bauer, Erich

AU - Dohmen, Elias

AU - Fouks, Bertrand

AU - Heckenhauer, Jacqueline

AU - Huylmans, Ann Kathrin

AU - Jones, Alun R. C.

AU - Stolle, Eckart

AU - Harrison, Mark C.

PY - 2024/6/1

Y1 - 2024/6/1

N2 - Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.

AB - Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.

UR - http://www.scopus.com/inward/record.url?scp=85194999865&partnerID=8YFLogxK

U2 - 10.1007/978-1-0716-3838-5_16

DO - 10.1007/978-1-0716-3838-5_16

M3 - Chapter

SN - 978-1-0716-3837-8

SN - 978-1-0716-3840-8

T3 - Methods in Molecular Biology

SP - 473

EP - 514

BT - Comparative Genomics

A2 - Setubal, João Carlos

A2 - Stadler, Peter F.

A2 - Stoye, Jens

PB - Humana Press

CY - New York, NY

ER -

Comparative Evolutionary Genomics in Insects

Abstract

Publication series

Funding

Access to Document

Other files and links

Embargoed Document

Fingerprint

Cite this