assemblies:2015:mitochondrion_assembly
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assemblies:2015:mitochondrion_assembly [2015/07/23 04:41] ndudek [Primer design for PCR to close gaps] |
assemblies:2015:mitochondrion_assembly [2015/07/27 03:18] karplus [PCR results] added full citations with links and mentioned scallops |
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| - Some kind of technical error or PCR artifact. | - Some kind of technical error or PCR artifact. | ||
| - The smaller contig may be a nump that, for some reason, circularized. Supporting this theory (possibly) is that if you blast the larger contig against the //Albinaria caerulea// genome, it looks like we have nearly the entire mitochondrial genome, expect for an ~800bp region (see dot plot below). This is only slightly shorter than the fragment amplified with the PCR above. Given that molluscs seem to have fairly conserved mitochondrial genome sizes of ~14,000bp, if both fragments are truly mitochondrial it means the total length must be over 16,309bp, which is unexpectedly large and may be incorrect. On the other hand, if the second largest contig is a nump, you would likely expect it to have some sequence similarity to the largest contig, but blasting them against each other finds no significant sequence similarity. Additionally, I used [[http://dogma.ccbb.utexas.edu/|DOGMA]] to do a preliminary annotation of both contigs, and it predicted that the largest carries the cox1 and cox 3 genes, whereas the second largest contig carries the cox2 and cob genes, so they appear to be complimentary. | - The smaller contig may be a nump that, for some reason, circularized. Supporting this theory (possibly) is that if you blast the larger contig against the //Albinaria caerulea// genome, it looks like we have nearly the entire mitochondrial genome, expect for an ~800bp region (see dot plot below). This is only slightly shorter than the fragment amplified with the PCR above. Given that molluscs seem to have fairly conserved mitochondrial genome sizes of ~14,000bp, if both fragments are truly mitochondrial it means the total length must be over 16,309bp, which is unexpectedly large and may be incorrect. On the other hand, if the second largest contig is a nump, you would likely expect it to have some sequence similarity to the largest contig, but blasting them against each other finds no significant sequence similarity. Additionally, I used [[http://dogma.ccbb.utexas.edu/|DOGMA]] to do a preliminary annotation of both contigs, and it predicted that the largest carries the cox1 and cox 3 genes, whereas the second largest contig carries the cox2 and cob genes, so they appear to be complimentary. | ||
| - | - The banana slug could possibly have a mitochondrial genome that is present as separate mini circular chromosomes, as seen in the human body louse, //Pediculus humanus// (see "The single mitochondrial chromosome typical of animals has evolved into 18 mini chromosomes in the human body louse, //Pediculus humanus//, by Shao //et al//., 2009). This could explain why both contigs circularized with the PCR that was run. However, it is probably too early to say whether this circularization is really "valid" or not. This is something that will be examined in greater detail in the future. | + | - The banana slug could possibly have a mitochondrial genome that is present as separate mini circular chromosomes, as seen in the human body louse, //Pediculus humanus// (see [[http://genome.cshlp.org/content/19/5/904.short|"The single mitochondrial chromosome typical of animals has evolved into 18 mini chromosomes in the human body louse, Pediculus humanus", by Shao et al., doi:10.1101/gr.083188.108 Genome Research 2009. 19: 904-912]]). This could explain why both contigs circularized with the PCR that was run. However, it is probably too early to say whether this circularization is really "valid" or not. This is something that will be examined in greater detail in the future. Note: [[http://genome.cshlp.org/content/19/5/700.full|‘Why genomes in pieces?’ revisited: Sucking lice do their own thing in mtDNA circle game. David M. Rand, |
| + | Genome Research. 2009. 19: 700-702. doi:10.1101/gr.091132.109]] lists other animals with multi-chromosome mitochondria, including a mollusk (scallop). | ||
| {{:assemblies:2015:longest_vs_a_caerulea.png?200|}} | {{:assemblies:2015:longest_vs_a_caerulea.png?200|}} | ||
| The mitochondrion assembly is being worked on by Natasha Dudek (natasha@dudek.org) from Team 5: Discovar //de novo//. | The mitochondrion assembly is being worked on by Natasha Dudek (natasha@dudek.org) from Team 5: Discovar //de novo//. | ||
assemblies/2015/mitochondrion_assembly.txt · Last modified: 2015/09/16 01:30 by ndudek
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