Table 1. Primers Used to Amplify Specific Regions of the LSU rRNA Gene from Oyster (Crassostrea virginica) Genomic DNA and cDNA Template.

Primers marked with * are from reference 37. The final set of primers was used to amplify scallop (Argopecten irradians) genomic DNA and cDNA, and would amplify in C. virginica cDNA if the fragments were spliced post-transcriptionally.
Region Primer 5' to 3' Oligonucleotide Sequence Product Length Annealing Temperature
5' portion mt168-F * GGATTCTGTTTGTCCGCAGCATT 233 bp 50 °C
mt169-R * CACCATATAGCTATCTTTAGTTGA
3' portion mt89-F * CAGTACCTGCCCAGTGCGACAA 494 bp 58 °C
16SBR CCGGTCTGAACTCAGATCACGT
Full LSU rRNA dCv-Ai-LSU-f CTTTWGCAKMATGGCYTTWTGAG ~773 bp in C. virginica
748 bp in A. irradians
55 °C
dCv-Ai-LSU-r CACGGGGTCTTCTTGTCTWWCTTT


Table 2. Summary of Large Subunit Molecular Characteristics for Crassostrea virginica, C. gigas, and C. hongkongensis.

  Measurement C. virginica [37] C. gigas [37] C. hongkongensis [38, 39]
Large Subunit, 5' Length (nt) 748 587 605
Percent A+T 65.9 69.4 67.9
Percent G+C 34.1 30.6 32.1
Large Subunit, 3' Length (nt) 719 713 712
Percent A+T 61.4 61.4 62.1
Percent G+C 38.6 38.6 37.9


Table 3. Percent Sequence Similarity between Crassostrea virginica, C. gigas, and C. hongkongensis.

* Similarities for the LSU 5' and LSU 3' are presented above and below the diagonal respectively.
LSU * C. virginica [37] C. gigas [37] C. hongkongensis [38, 39]
C. virginica - 65.0 65.0
C. gigas 83.0 - 89.0
C. hongkongensis 84.0 96.0 -


References:

Reference numbers refer to the numbering system used in the published manuscript.
# Reference Reference Links
37. Milbury C.A. and Gaffney P.M. (2005).
Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica.
Marine Biotechology, 7(6):697-712.
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38. Yu Z., Wei Z., Kong X., and Shi W. (2008).
Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis - a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea?
BioMed Central Genomics, 9:477.
PM | PMC | DOI ]
39. Ren J., Liu X., Zhang G., Liu B., and Guo X. (2009).
"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes: comment.
BioMed Central Genomics, 10:84.
PM | PMC | DOI ]