Research project for summer training

[MManee]

Project title: Comparative analysis of camel mitochondrial genomes

The aims of this project are to:

• annotate the mitochondrial genome of Arabian camel
  • the mitochondrial sequence of Arabian camel is here: link
    • compare the mitochondrial genome of Arabian camel with the mitochondrial genome of wild two-humped camel
    • the mitochondrial sequence of wild two-humped camel is here: link
    • reference paper for the mitochondrial sequence of wild two-humped: link
    • we need to replicate most of results in this main reference paper link using the mitochondrial sequence of Arabian camel
    • @atalgarni and @1sar2003 will help you out with this project
    • the duration of this work is a month (Deadline is 16 August 2018)
    • this paper might be useful: 24 camel mitogenome and Cetonurus globiceps

[MManee]

• In main reference paper, there is a sentence:

Secondary structure models of the tRNA genes in the two newly sequenced mitochondrial genomes were predicted using the Mitos WebServer (Fig. 3)

• In last column called structure, click on svg and generate secondary structure of the tRNA genes only
• so please use Mitos WebServer to generate figure like figure 3

[MManee]

TO DO

• [ ] annotation of camel mitochondrial genome [Shahad, Riyof and Maha]
• [x] identify start and stop codon of Protein-coding genes [Abdulamek]
• [x] identify the predicted secondary structures of transfer RNA genes (tRNA) [Shahad, Riyof and Maha]
• [ ] identity intergenic spacers between the mitochondrial genes [Shahad, Riyof and Maha]
• [ ] calculate AT-skew and GC-skew for whole mitochondria genome and protein coding genes [Shahad, Riyof and Maha]
• [ ] perform multiple sequence alignment between camel mitochondrial genomes and generate phylogenetic tree [Shahad, Riyof and Maha]

  the checklist will be updated on a regular basis. Please check this regularly for updates

[MManee]

to identity intergenic spacers between the mitochondrial genes:

• you need to convert mitochondria genome and mitochondria genes in FASTA format to bed format using “faidx” function in Samtools:
  • for example, to convert mitochondria genome to bed format faidx --transform bed camel_mitochondria_genome.fasta > camel_mitochondria_genome.bed
• you will be able then to retrieve the intergenic regions in bed format using bedtools subtract bedtools subtract -a camel_mitochondria_genome.bed -b camel_mitochondria_genes.bed > intergenic_regions.bed

[riyof]

@amer1404 @MManee We think we have a problem in installing samtools because when we convert the fasta file into bed format the new bed file became empty.

[MManee]

Installation Page of SAMtools Link

[bioinfo2016]

To know what is the error type: faidx --transform bed camel_mitochondria_genome.fasta > camel_mitochondria_genome.bed 2>errorfile

[MManee]

this comment may be useful for you to run your bedtools commands globally in your machines Go to comment

[MManee]

• @Manal-Alshehri, please teach Shahad, Maha and Riyof how to use MAFFT to perform multiple sequence alignment (MSA):
  • and use the output of MAFFT to generate the phylogenetic tree
• they have so far more than 30 mitochondrial genomes from different camel breeds

[Manal-Alshehri]

@MManee Sure, I can set up a meeting and explain everything related to MAFFT. @riyof, please contact me directly on (m-sher@hotmail.com) so we can arrange time/place to meet soon.

[atalgarni]

• The start and stop codon of Protein-coding genes have been added to the latex version. I have added the intergenic/overlap region too.
• I have added another table generated from tRNAScan-SE website confirming the start stop and annotation of tRNAs generated by Mitos webserver.

[Manal-Alshehri]

@MManee I used the software MEGA to compare the Relative synonymous codon usage (RSCU) for Camelus Dromedary and Camelus bactrianus (as Figure.1 in the reference paper). I created two charts for illustration and interpret them in the section "Materials and Methods: Comparative analysis of the mitochondrial genomes"

[Manal-Alshehri]

@MManee We are in the middle of the phylogenetic analysis for the 32 species. We already performed the sequence alignment in MAFFT, should we adopt the phylogenetic tree provided by MAFFT? Or use another sophisticated tool (like BEAST) to reconstruct the tree?