Description

This track shows the multiple genome alignment of ten Drosophila genomes. It also shows the measurements of evolutionary conservation using phastCons and phyloP from the Phylogenetic Analysis with Space/Time models (PHAST) package.

Methods

Whole Genome Alignments

The whole genome alignments were produced using LAST, and then processed by the last-split and last-postmask programs to identify orthologous regions between the nine Drosophila genomes and the D. willistoni genome assembly. The split-alignments between nine Drosophila genome assemblies and Drosophila willistoni were combined into a multiple sequence alignment using ROAST. The ROAST alignments were processed using the utilities developed by the UCSC Genome Bioinformatics Group for display on the UCSC Genome Browser.

The following table shows the ten Drosophila genome assemblies used to construct the ROAST Alignments track:

Assembly Name	Species	Isolate	Accession Number
DwilRefSeq2	Drosophila willistoni	14030-0811.24	GCF_018902025.1
ASM1815034v1	Drosophila equinoxialis	14030-0741.00	GCA_018150345.1
ASM1815213v1	Drosophila paulistorum	14030-0771.06	GCA_018152135.1
ASM1815108v1	Drosophila tropicalis	14030-0801.00	GCA_018151085.1
ASM1890393v1	Drosophila insularis	jp01i	GCA_018903935.1
ASM1815037v1	Drosophila sturtevanti	14043-0871.01	GCA_018150375.1
ASM1890361v1	Drosophila neocordata	14041-0831.00	GCA_018903615.1
ASM1890357v1	Drosophila saltans	14045-0911.00	GCA_018903575.1
ASM1815127v1	Drosophila prosaltans	14045-0901.02	GCA_018151275.1
dm6	Drosophila melanogaster	iso-1	GCF_000001215.4

Phylogenetic Tree Model

The non-conserved model used by phastCons and phyloP was constructed by the phyloFit program from the PHAST package using the general reversible (REV) substitution model.

PhastCons Conservation

Conserved elements were identified by phastCons using an expected length of 45 and a target coverage of 0.3. The conserved model is defined as a scaled version of the non-conserved model with the scaling factor rho of 0.4.

PhyloP Conservation

The conservation score for each site of the alignment was determined by phyloP using the likelihood ratio test (LRT) and the CONACC mode. Sites with positive scores indicate conservation while sites with negative scores indicate acceleration.

References

Finet C, et al. DrosoPhyla: Resources for drosophilid phylogeny and systematics. Genome Biol Evol. 2021 Aug 3;13(8):evab179.

Frith MC, Kawaguchi R. Split-alignment of genomes finds orthologies more accurately. Genome Biol. 2015 May 21;16(1):106. doi: 10.1186/s13059-015-0670-9.

Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan;12(1):41-51.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.