Reassignment of Drosophila willistoni Genome Scaffolds to Chromosome II Arms

Abstract

Drosophila willistoni is a geographically widespread Neotropical species. The genome of strain Gd-H4-1 from Guadeloupe Island (Caribbean) was sequenced in 2007 as part of the 12 Drosophila Genomes Project. The assembled scaffolds were joined based on conserved linkage and assigned to polytene chromosomes based on a handful of genetic and physical markers. This paucity of markers was particularly striking in the metacentric chromosome II, comprised two similarly sized arms, IIL and IIR, traditionally considered homologous to Muller elements C and B, respectively. In this paper we present the cytological mapping of 22 new gene markers to increase the number of markers mapped by in situ hybridization and to test the assignment of scaffolds to the polytene chromosome II arms. For this purpose, we generated, by polymerase chain reaction amplification, one or two gene probes from each scaffold assigned to the chromosome II arms and mapped these probes to the Gd-H4-1 strain’s polytene chromosomes by nonfluorescent in situ hybridization. Our findings show that chromosome arms IIL and IIR correspond to Muller elements B and C, respectively, directly contrasting the current homology assignments in D. willistoni and constituting a major reassignment of the scaffolds to chromosome II arms.

Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa

“…As a note, the D. willistoni caf1 (GCA_000005925.1) and D. willistoni 17 (GCA_018903445.1) assemblies will hereby be referenced as wil_caf1 , and wil_17 , respectively. First, we identified chromosomal locations of wil_caf1 assembly scaffolds, using data from previous studies ( Supplementary Table 9 ) ( Schaeffer et al 2008 ; Garcia et al 2015 ). In an attempt to use a more contiguous reference, we used Satsuma2 ( https://github.com/bioinfologics/satsuma2 ) ( Grabherr et al 2010 ) to find syntenic scaffolds between the wil_caf1 and wil_17 assemblies ( Supplementary Table 10 ).…”

Characterizing the transcriptional expression and in situ localization of the Dnmt2 gene in Drosophila willistoni

“…The location of the probe hybridization signal was determined to be at the distal region of the chromosome II left arm (IIL), specifically in section 55C ( Figure 5A and 5B). The IIL arm of D. willistoni corresponds to the Muller B element, according to a previous study [37]. On FlyBase search tool [38], However, although such species have genomic methylation, this is still at low global levels and Dnmt2 biological function has been fervently discussed [40,41].…”

“…The gene is located in the arm IIL (Muller B element), like in D. melanogaster and D. pseudoobscura, where it was possible to ascertain the position of the gene, it is present in B element. This is a very important aspect because we present here the determination of another gene marker in D. willistoni, following previous work [37], which will help in the organization of the D. willistoni scaffolds regarding the physical position of the genes in the chromosomes. [53].…”

Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach

“…Our research group has been studying several aspects of the chromosomal plasticity of D. willistoni ( Valente and Araújo, 1985 ; Valente et al. , 1993 ; Valente et al , 2003 ; Rohde and Valente, 2012 ; Garcia et al, 2015 ). The goal of the present study was to contribute to understanding the high degree of variability of D. willistoni over its wide geographical distribution.…”