As more and more genomes are being sequenced the likelihood of having a close relative being sequenced is rising.
So lets say I have a non-model species Chela cachius and I want to find the closest species that has a sequenced genome. Looking at the species tree the answer is most likely Danio rerio (Ensembl GRCz11).
Is there a software tool for it? So that if I have e.g Limanda limanda it gives me the most likely candidates for closest available genome.
Dear Richard,
I can recommend a few tools in order to help you to locate genomes closest related to that of your pet organism. There are a few useful databases available at the NCBI. They are the Taxonomy database, to identify those species most closely related to your pet organism. There is also the Genome database where you can browse organisms for which there are already genomes available and finally there is also a BLAST interface that allows you, in the case you have already gene sequences of your pet at hand, to carry out BLAST searches in the Genome database to identify those genomes most closely related to that of your own pet. Here follow the links:
https://www.ncbi.nlm.nih.gov/taxonomy
https://www.ncbi.nlm.nih.gov/genome/
https://blast.ncbi.nlm.nih.gov/Blast.cgi
Dear Richard Meitern,
As mentioned by Fred R. Opperdoes, I think that the best tool is indeed BLAST. If NCBI nucleotide database has some sequenced genes for your species of interest, you can use this information to do a BLAST search in the NCBI genome database, and you do not need to wait for your genome assembly results.
If your organism of interest still does not have any available sequences, I recommend that you do a genome assembly, and then: i) retrieve the sequences of marker genes from your genome assembly (by doing a local BLAST with sequences of species of the same genus that you can obtain in NCBI nucleotide database) and do an online BLAST of these sequences using the NCBI genome database; OR ii) get some contigs of your assembly and do an online BLAST on the genome database. This last approach is perhaps more time consuming if your contigs are very big.
As I think that this may be helpful for some people, I want to add that JGI database has a great "Tree of Life" interface (https://genome.jgi.doe.gov/portal/pages/tree-of-life.jsf), where we can zoom in in phylogenetic trees which comprise all sequenced species present in their database. However, although presenting very accurate assemblies, this database does not comprise all the genomes available in NCBI database, and therefore there is the risk of not detecting the closest sequenced species. It is important to mention, that JGI also have some private data, meaning that it may give you information on genomes that are still not available but that you can use after contacting the authors.
Best,
Richard Meitern
Option 1: https://tygs.dsmz.de/: You can upload your genome at Type strain Genome server and they will create a phylogenetic tree and then you can get a close idea of which strains are the phylogentic neighbours of your strain (bacteial) Not sure what organism you have.
Option 2: Use https://www.ezbiocloud.net/contents/genome. You can upload your genome into this database and it can show you closest neighbours.
Option 3. Extract the 16sRNA sequence from the WGS of your strain (you can do that using EZbiocloud-very easy step after you upload the genome) OR you can use annotation services like RAST and from there can extract the 16sRNA sequence. Later, using EZbiocloud 16sbasedID, you will find the most closely relates species to your strain. As convention, a cutoff of 98-99% is considered i.e. if species is below this cut of value, it is a novel species , if equal or above, it belongs to same species.
Option 4: RAST server: IF you annotate the genome using RAST, it provides an option to see closest neighbours (but in my opinion is not always the best and close hits. usually the first strain is close enough).
Hope it helps.
Richard Meitern Today while reading loads of paper regarding the best tool for comparative genomics, I came across PATRICK ( https://www.patricbrc.org/). This is an excellent web-based software that allows user to
1.add their own genome sequences
2. Phylogenetic tree construction: It allows you to create a codon - based phylogenetic tree. Provides flexibility to choose as many codons as you would like to create a tree with; with a possibility to add even more than 100 strains/species to create a phylogenetic tree (with just one tick option, without having the need to find each genome or gene sequences for the set of strains you want to analyze. So, based on that phylogenetic tree you can easily figure out which are the most closely related neighbours. Not just that, you can even find out most closely related Genus.
2. Similar genome finder : https://www.patricbrc.org/app/GenomeDistance . This shows a a set of genomes matching the specified similarity criteria
I hope all this helps.
Timsy
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