Computational protocol: Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome

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Protocol publication

[…] Several potential scaffold adjacencies with no gaps were identified during physical mapping. For “gluing” An. atroparvus genomic scaffolds, several dozen genes from the candidate scaffolds’ ends were selected. Orthologous genes for these genes in the An. gambiae and An. albimanus genomes were identified using BioMart (http://biomart.vectorbase.org/biomart/martview/). If orthologs for all An. atroparvus genes from candidate scaffolds’ ends were located continuously in single scaffolds of An. gambiae and An. albimanus, An. atroparvus scaffolds were considered adjacent to each other without gaps. [...] The BioMart service (http://biomart.vectorbase.org/biomart/martview/) was used to extract the set of all annotated orthologous genes for An. atroparvus (AatrE1 genome assembly v.86.1), An. albimanus (AalbS2 genome assembly v.86.2), and An. gambiae (AgamP4 genome assembly v.86.4). These data were prepared using R and RStudio IDE to generate an input file for GRIMM-Synteny v. 2.02 []. During the preparation of the data, coordinates of the An. atroparvus genes within genomic scaffolds were converted into coordinates on the An. atroparvus chromosomes. GRIMM-Synteny takes coordinates of orthologous genes of species and forms syntenic blocks based on specified parameters, such as minimum block size and gap threshold (a maximum distance between genes in a synteny block). Synteny blocks obtained by GRIMM-Synteny were visualized using genoPlotR []. The Multiple Genome Rearrangement (MGR) program [] was used to determine the number and types of rearrangements that caused the synteny block reshuffling among three species. To run the random model for synteny blocks, we obtained the sample of random breaks by generating (N-1)*2 random numbers from 0 to M, where N and M are a mean number of synteny blocks and a mean length of genomes (base pairs) in three species, respectively. We arranged all coordinates of random breaks ascending and measured the length between each break. To simulate random distances between synteny blocks, we randomly removed one half of the samples. Eventually, we obtained a sample of lengths for N random synteny blocks. […]

Pipeline specifications

Software tools BioMart, MGRA, genoPlotR, MGR
Databases VectorBase
Applications Genome annotation, Phylogenetics, Genome data visualization
Organisms Anopheles atroparvus, Danio rerio
Diseases Malaria