Contig by contig linear sequencing by using Sanger,s method of genome sequencing. Align and arrange data by using through put methods line Micro-array for gene functions and expression.  

Thanks Ravi and Sezer, It is hard to design primers to sequence the mithchondrial genome because it have long repeat sequence and varied structure among different species. so arranging the genome is difficult.

It is much easier than it used to be with a combination of Illumina and PacBio data. If you take total genomic DNA and get about 50 million Illumina paired-end reads you can assemble all the data in Velvet and find the mtDNA by coverage--it will have about half the coverage as the cpDNA. Then use the Illumina data to correct the SMRT cell of PacBio data (also from total genomic DNA) using the LSC package and use the corrected reads to scaffold together the contigs from Velvet. You will only end up using a few of the long PacBio reads (longer than 10 kb) that span the large repeats to assemble the mtDNA into a single master circle.

Plants mitogenomes are have very variable structure and gene content. It's hard to point out "the best" strategy. For the most of plant families, combined Ilumina + PacBio (or ON) sequencing will be necessary. Sometimes combined pair-end + mate-pair with long inserts could give enough data to proper assembly. For lower plants de novo sequencing mitogenomes are much simpler.

Dear All,

I want to assembled mitochondrial genome from Illumina data of 150 bp Pair end libraries. I have got two file of 5 GB each in which about 29 millions read are present. When I have done Bowtie alignment with the closed relative, only about 60,000 read aligned into reference genome.

When I have combined these raw read for just to got a draft sequence, I got a file with about 2,98,000 bp in which 45 gene were predicted.

Now, Is it possible to get the whole mitochondrial genome from this data?