Complete mitochondrial genome sequence of Coccinella septempunctata (nine-spotted & eleven-spotted ladybird)

[MManee]

link to a reference paper: mitochondrial genome of the two-humped camel

TODO:

• [x] collection of the samples
• [ ] DNA extraction
• [ ] DNA sequencing
• [ ] assembly of DNA sequences
• [ ] phylogenetic analysis

[SULTAN-ALHARBI]

@amer1404 @MManee Dear All this is Accession Number [GenBank: EF212038] for A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus) We can compare it with: The complete mitochondrial genomes 1) L. pacos [Gen- Bank:Y19184] 2) Bos taurus [GenBank:AY526085] 3) Sus scrofa [GenBank:AF034253] 4) Mus musculus [Gen- Bank:AY172335]

[MManee]

• thank you sultan for posting the accession number of complete mitochondrial genome of the two-humped camel
• It would be great if we have the raw data for the same genome or any mitochondrial genome to start building our own assembly pipeline (@amer1404 will start working on it)

[SULTAN-ALHARBI]

Sequencing Mitochondrial Genome of P. concolor couguar: Accession Number: SRX2187549 from Illumina HiSeq 2500 How to download a raw data go to NCBI website -----> in search icon paste the Accession Number-----> choose database (SRA) then search you will get the raw data

[MManee]

• we can annotate three mitochondrial genomes of Arabian camel:
  • the mitochondrial genome from UAE (accession number: EU159113):
  • They didn't annotate the genome (not published yet)
  • the genome data can be found here: UAE mitochondrial genome
  • the mitochondrial genome from Morocco (accession number: JN632608)
  • they only studied the evolution of a number of mitochondrial genomes including the genome from Morocco (link to paper: evolution)
  • They didn't annotate the genome (not published yet)
  • the genome data can be found here: Morocco mitochondrial genome
  • we can sequence and annotate the mitochondrial genome from Saudi as we planned before
  • so we have three mitochondrial genomes in total to work on
• I suggest to work on annotating the mitochondrial genomes from UAE and Morocco
  • the template paper is this: mitochondrial genome of the two-humped camel

[MManee]

• for annotation of mitochondrial genomes from UAE and morocco:
  • there are many tools can be used to annotate protein-coding and rRNA genes
  • two recent papers were added here (should help you with the analysis): link to papers
  • you can initially annotate it online using Mitos Web Server Mitos Web Server

[MManee]

• more papers about Arabian camel & sequencing and annotation of mitochondrial genomes were added here: https://github.com/kacst-bioinfo-lab/labwork/tree/master/doc/shared/mitochondrial_genome

[atalgarni]

Please check this paper... it was recently published on nature scientific reports https://www.nature.com/articles/srep44300

this paper used Mitos web server to identify tRNA,,,,,, the assembly was done by Lasergene software (DNAStar, Inc., USA, NewYork) I think sultan have a license we could use.

for more info please refer to this paper__methods and materials

I am now using the same Mito server for the data sent by Manee Coccinella septempunctata, complete genome JQ321839.1

job has been completed you could check the results at http://mitos.bioinf.uni-leipzig.de/result.py?hash=tbRWezAY

[amer1404]

How to sequence and annotate insect mitochondrialgenomes for systematic and comparative genomicsresearch

CAMERON-2014-Systematic_Entomology.pdf

[amer1404]

create Annotation of the Episyrphus balteatus mitochondrial genome table for hoverflies Episyrphus balteatus and Eupeodes corollae paper

Updated amer 2.zip

[amer1404]

Table 4. Nucleotide composition in regions of Muscomorpha mitochondrial genomes. table4.zip

Total length 16643

C count: 4423   26.5757375473172 % 
A count: 5132   30.8357868172805 % 
G count: 2578   15.4899957940275 % 
T count: 4510   27.0984798413748 % 
AT (%) :57.9342666586553

[MManee]

New thread is now open to investigate and annotate camel mitochondrial genome #23