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--- assemblies:2015:mitochondrion_assembly [2015/07/27 03:18]
karplus [PCR results] added full citations with links and mentioned scallops
+++ assemblies:2015:mitochondrion_assembly [2015/09/16 01:30] (current)
ndudek [PCR results]
@@ Line 33: / Line 33: @@
 |mitochondrion_iteration2_SW018-9_discovar| 48K | 45,494 | 114 | 9,030 | 9,030 | 15,548 | 0 | 436X |
-For comparison, the mitochondrion size of the closest related molluscs that have mitochondrion assemblies are 14,100bp (grove snail - //Cepaea nemoralis//) and 14,130bp (land snail - //Albinaria coerulea//)
+For comparison, the mitochondrion size of the closest related molluscs that have mitochondrion assemblies are 14,100bp (grove snail - //Cepaea nemoralis//) and 14,130bp (land snail - //Albinaria coerulea//). But there are mollusk mitochondrial genomes that are much larger: sea scallop //Plactopecten magellanicus// is reported to have 30.6-30.7kbp ([[http://link.springer.com/article/10.1007/s00239-007-9016-x#page-1|David R. Smith and Marlene Snyder. Complete Mitochondrial DNA Sequence of the Scallop Placopecten magellanicus: Evidence of Transposition Leading to an Uncharacteristically Large Mitochondrial Genome. J Mol Evol (2007) 65:380–391 doi:10.1007/s00239-007-9016-x]]).
 It looks as though the majority of the mitochondrion is in two contigs in the assembly using both the SW018 and SW019 assemblies. One of these contigs is 12,884bp and the other (which is the second largest contig) is 3,425bp.
@@ Line 208: / Line 209: @@
 {{:assemblies:2015:longest_vs_a_caerulea.png?200|}}
+August 2015
+PCR products were sent for Sanger sequencing. Something went wrong - the result was largely "N"s. I checked whether I could improve calls by looking at the chromatogram, but did not have significant success. Below is an example of what the chromatogram looked like. I will be re-sending the PCR products for sequencing.
+{{:assemblies:2015:chromatogram_mito_august2015.png?200|}}
+September 2015
+PCR products were sent for sequencing a second time, this time after a size selection on the strongest band. Results were essentially the same.
 The mitochondrion assembly is being worked on by Natasha Dudek (natasha@dudek.org) from Team 5: Discovar //de novo//.

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