DOI: 10.5061/dryad.mw6m90617
title: Data from: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences

description: Background During evolution, genes can experience duplications, losses,
 inversions and gene conversions. Why certain genes are more dynamic than
 others is poorly understood. Here we examine how several Sgs genes
 encoding glue proteins, which make up a bioadhesive that sticks the animal
 during metamorphosis, have evolved in Drosophila species. Results We
 examined high-quality genome assemblies of 24 Drosophila species to study
 the evolutionary dynamics of four glue genes that are present in D.
 melanogaster and are part of the same gene family – Sgs1, Sgs3, Sgs7 and
 Sgs8 – across approximately 30 millions of years. We annotated a total of
 102 Sgs genes and grouped them into 4 subfamilies. We present here a new
 nomenclature for these Sgs genes based on protein sequence conservation,
 genomic location and presence/absence of internal repeats. Two types of
 glue genes were uncovered. The first category (Sgs1, Sgs3x, Sgs3e) showed
 a few gene losses but no duplication, no local inversion and no gene
 conversion. The second group (Sgs3b, Sgs7, Sgs8) exhibited multiple events
 of gene losses, gene duplications, local inversions and gene conversions.
 Our data suggest that the presence of short "new glue" genes
 near the genes of the latter group may have accelerated their dynamics.
 Conclusions Our comparative analysis suggests that the evolutionary
 dynamics of glue genes is influenced by genomic context. Our molecular,
 phylogenetic and comparative analysis of the four glue genes Sgs1, Sgs3,
 Sgs7 and Sgs8 provides the foundation for investigating the role of the
 various glue genes during Drosophila life.
description: <strong>Supplementary
 Files</strong> File S1.
 Compressed zip file of the gene annotations (GenBank .gb files, inputs for
 Easyfig) of large genomic regions containing all the
 <em>Sgs</em> genes and their neighboring genes in the 24
 studied species. File S2.
 Fasta file of all the Sgs amino acid sequences used to create Figure 1B
 and Figure S1. File S3.
 Compressed zip file of reference and corrected nucleotide sequences used
 to create Figure S2. File S4.
 Compressed zip file of Sgs protein alignments (fasta.files) used to
 compute phylogenetic trees and make Weblogo figures. File S5. Sgs coding sequence length in bp for
 species having an Sgs3x copy (.csv file, input for R script
 sgs_size.R). File S6. Sgs
 coding sequence length in bp for species not having an Sgs3x copy (.csv
 file, input for R script sgs_size.R). File S7. Compressed zip file of comparisons
 between pairs of large genomic regions (.out files obtained as outputs
 from Easyfig). File S8. Table
 of pairwise percentage of identity between several Sgs1 and Sgs3
 amino-acid sequences (.csv). File S9. Compressed zip file of the repeats
 annotations (.csv files) obtained with FindRepeat in Geneious on large
 genomic regions for D. melanogaster <em>Sgs1, Sgs3/7/8, Sgs3x, D.
 teissieri Sgs3/7/8, D. subobscura Sgs3, D. eugracilis
 Sgs3.</em> File S10.
 Compressed zip file of new glue protein alignments (.fasta files) used to
 make Fig. S9. File S11. Fasta
 file of all the <em>Sgs</em> nucleotide sequences studied
 here. File S12. Fasta file of
 the 154 <em>ng</em> nucleotide sequences found at loci 68C11
 and 68C13. File S13. Fasta
 file of the 41 <em>ng</em> nucleotide sequences found at loci
 3C11-12, 28E6-28E7, 87A1 and 88C3-4. File S14. Compressed zip file of all the R
 scripts (.R files) used to create the figures. File S15. Bam file of raw reads mapped to
 <em>D. rhopaloa</em> Sgs1 corrected nucleotide sequence, used
 to create Figure S2A. File
 S16. Bam file of raw reads mapped to <em>D. ficusphila</em>
 Sgs1 reference nucleotide sequence, used to create Figure S2B.
 File S17. Bam file of raw reads mapped
 to <em>D. biarmipes</em> Sgs3x corrected nucleotide sequence,
 used to create Figure S2C.