Hi,
I will be whole genome resequencing multiple individuals from each of a set (> 2) of related species, followed by aligning each to its own species' chromosome-level reference genome assembly. From that starting point, I would like to identify homologous sequence among species for comparative population genomic analyses. I'm equally interested in syntenic and non-syntenic regions (a nice bonus would be if presence/absence of synteny could be scored), and in genic and intergenic regions. Basically, I want to keep as much of the genome as possible. Questions:
- Is there a well-established protocol for identifying a set of homologous regions among multiple species, given this starting point? i.e. to cross-reference the potentially different locus names among all species, after they've been aligned to their intraspecific reference genome?
- Alternatively, is it necessary to first assemble the reference genomes against each other in order to identify homologous sequence, followed by assembling my multiple resequencing samples to the joint genome assembly?
Thanks in advance! Richard.
It probably depends on what type of organism. Are you studying prokaryotes, or eukaryotes? How much diversity is found in a given "species". For one example, there is a vast difference in the diversity of gene order on chromosomes in bacteria considered to be in the E. coli species and those considered to be Clostridium botulinum.
Thanks Brian. They're insects with fairly small diploid genomes. It's unclear at this stage how much genetic diversity is present.
You are describing "phylogenomics"; creating phylogenies from large numbers of genes from each sample. The PhyLUCE software is used for studying pylogeny based on hundreds to thousands of quite short "ultra conserved elements" which is useful for comparisons of groups of organisms (such as insects) whose common ancestor dates back hundreds of millions of years ago.
These papers should be of use to you:
Article Advances using molecular data in insect systematics
https://phyluce.readthedocs.io/en/latest/tutorials/index.html
https://pubmed.ncbi.nlm.nih.gov/31546095/
Article Phylogenomics from Whole Genome Sequences Using aTRAM
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9544963/
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