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.