A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira

Abstract

Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila 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 data set 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 6 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.

Keywords: Drosophila madeirensis; HiFi; genome assembly; inversion breakpoint.

Fig. 1.

Overview of D. madeirensis and its genome. a) A phylogenetic tree and pictures of fly samples of the species belonging to the D. subobscura subgroup. b) Distribution of D. madeirensis. D. madeirensis is endemic to the island of Madeira in the Atlantic Ocean. The map was modified from the digital map published by the Geospatial Information Authority of Japan. c) Representation of the distribution of genes and repeat sequences on each D. madeirensis assembled chromosome. Chromosomes are ordered by their size. The proportion of elements per each 100-kb nonoverlapping window is plotted as a histogram. The y-axis range is set to 0–1. The circular genome map was produced using the circlize R package (Gu et al. 2014).

Fig. 2.

Harr plot made with minimap2 (Li 2018) whole-genome alignment between D. madeirensis and D. subobscura genome sequences. Sequences aligned in forward and reverse orientations are represented by upward-sloping and downward-sloping lines, respectively.

Fig. 3.

Detailed characterization of inversion breakpoints. Harr plots of D. madeirensis and D. subobscura genome sequences at the O₄ a), A₆ b), and A_h4 c) breakpoints are shown. Sequences aligned in forward and reverse orientations are represented by upward-sloping and downward-sloping lines, respectively. The dotted lines indicate breakpoints of the inversions. Each filled rectangle represents a coding region of the D. madeirensis gene model.