Posted by & filed under Cgigas DNA Methylation.

One of the premises related to germline methylation in oysters is that genes with limited methylation will have more alternatively spliced products. One of our most robust identification of alternatively spliced genes is from the heat shock experiment, however methylation was assessed with array to ID DMRs. In order to gauge the relationship of germline methylation and alternative splicing I looked at all of our data and made the calls.

I simply looked at the 42 areas determined to be alternatively spliced in the three individuals and qualitatively made the call. For example..


Of the 42 genes, only 11 were determined have limited methylation.

scaffold1391:350297-393525 - High
scaffold1501:189-2280 -  Low-Medium
scaffold1546:22946-41272 - High
scaffold157:93056-102166 - High
scaffold157:288396-298950 - High 
scaffold1583:636568-663717 - High
scaffold1630:57333-61806 - Low
scaffold1643:190932-200778 - Low 
scaffold1670:360106-365501 - High
scaffold1750:71251-77856 - High
scaffold1009:677703-719650 - High
scaffold1009:990592-1008075 - High 
scaffold193:111771-117728 - High 
scaffold198:1032767-1055090 - Medium-High
scaffold198:1084454-1102022 - High
scaffold211:954418-990421 - Medium-High
scaffold351:641567-648889 - Low 
scaffold102:1297353-1322657 - Low-High
scaffold383:99975-117650 - Low-High
scaffold38366:25577-54928 - Low 
scaffold1024:1037898-1043721 - Medium-High
scaffold395:85069-105025 - High
scaffold399:120007-128313 - High
scaffold41228:55316-64219 - Low 
scaffold41858:126164-135361 - High
scaffold42366:124115-157800- High
scaffold42892:55315-57225 - Low 
scaffold42904:154963-177485 - High 
scaffold43208:19552-46201 - High 
scaffold43940:65971-85144 - High
scaffold452:65648-77493 - Low 
scaffold527:16020-64639 - Low 
scaffold588:178668-183438 - High
scaffold616:53220-63262 - Low 
scaffold828:110697-114691 - High
scaffold942:369690-377892 - High
scaffold1160:333463-390372 - Low-High
scaffold1213:118721-121110 - Low 
scaffold128:428337-438047 - Low 
scaffold1282:23471-48121 - Low 
scaffold13:4222-16204 - Low
scaffold1322:265134-304245 - High

The caveat is (there always seems to be one) is this list of alternative spliced genes is based on consistency across individuals, something we would predict NOT to see if this was truly a stochastic phenomenon.

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