Journal article
A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira
G3 : genes - genomes - genetics, Vol.14(9), jkae167
09/04/2024
DOI: 10.1093/g3journal/jkae167
PMCID: PMC11373663
PMID: 39031588
Abstract
Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, D. madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing dataset to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb, and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the six chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, D. madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing dataset to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb, and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the six chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.
Details
- Title: Subtitle
- A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira
- Creators
- Kenta Tomihara - National Institute of Information and Communications TechnologyAna Llopart - University of IowaDaisuke Yamamoto - National Institute of Information and Communications Technology
- Resource Type
- Journal article
- Publication Details
- G3 : genes - genomes - genetics, Vol.14(9), jkae167
- Publisher
- OXFORD UNIV PRESS INC
- DOI
- 10.1093/g3journal/jkae167
- PMID
- 39031588
- PMCID
- PMC11373663
- ISSN
- 2160-1836
- eISSN
- 2160-1836
- Grant note
- Japan Society for the Promotion of Science (JSPS): JP23KJ2210 Ministry of Education, Culture, Sports, Science and Technology (MEXT): JP21H04790
This work was supported by a Japan Society for the Promotion of Science (JSPS) Grant-in-Aid (no. JP23KJ2210) to K.T. and a Ministry of Education, Culture, Sports, Science and Technology (MEXT) Grant-in-Aid (no. JP21H04790) to D.Y. DAS:The raw sequence data have been submitted to DDBJ under accession numbers DRR528066 (genomic HiFi reads), DRR528092 (genomic short reads), and DRR528093-528099 (RNA-seq reads). The D. madeirensis genome assembly and gene models have been submitted to DDBJ under accession numbers AP029263-AP029373.
- Language
- English
- Electronic publication date
- 07/20/2024
- Date published
- 09/04/2024
- Academic Unit
- Biology
- Record Identifier
- 9984658349202771
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