To investigate if RrmiRs expansion accompanied SD events, we compared the genomic coordinates of the RrmiRs and SDs.
Then the expansion of this miRNA family could not have been promoted by early SD events in the evolutionary process.
But if the members from a miRNA family are present in the two SDs of an SD pair, it is likely that the miRNA family was expanded by the early SD events.
SD events can be evoked by hypoxia [1], [4], [21], ouabain [22], [1], [4], simulated ischemia [23], and increased [K+]o [1], [4], [21] with normal temperature, as well as hyperthermia [1].
Although previous reports have mentioned that novel miRNAs can be produced from miRNA gene duplication [4] [10], there is little known about the miRNAs that are produced and expanded in SD events.
Our main results suggest that repetitive elements contribute to the de novo origin of miRNAs, and that large SD events may also accelerate the expansion of miRNA families, including RdmiRs.
Detailed analysis has attributed several roles to SD events: creation of new genes in primates, expansion of multigene families, and triggering large scale chromosomal rearrangements in hominoid [ 44].
In view of the most abundant LINEs in the reptiles (Supplementary information, Table S5), we further examined the relationship between the SD and LINE distributions and found a significant positive correlation (r = 0.89; P = 0.001), suggesting that the SD events might be triggered by LINEs, which has also been demonstrated in mammals.
To test our hypothesis that, in addition to the effect of MER53 transposition, SD events may contribute to the expansion of the hsa-mir-1302 hsa-mir-1302 hsa-mir-1302egmental duplication data that were pre-computed by Bailey and his colleagues [ 66] and that we downloaded familyhe UCSC Genome Broweer [ 52].
A noteworthy observation from our analysis is the high content of organelle DNA (NUMTs and NUPTs) as part of Pinot Noir duplications repertoire suggesting that organelle DNA sequence integration, other than SD events, played an important role in grapevine nuclear genome evolution.
To study the temporal profile of SDs further, two important challenges remain: to know the start of the SD event in the microdialysis data and to detect the metabolism changes with high temporal resolution.
