Project description:High-throughput small RNA sequencing (sRNA-seq) has facilitated many discoveries, but extracellular sRNA (ExRNA) present unique analytical challenges that are not met by current software. Therefore, we developed a novel data analysis pipeline entitled, “TIGER”, which caters to exRNA. To demonstrate the power of this tool, sRNA-seq was performed on high-density lipoproteins (HDL), apolipoprotein B particles (APOB), bile, urine, and liver samples. TIGER was able to characterize approximately 60% of lipoprotein, and >85% of liver, bile, and urine sRNA-seq depth, a significant advance compared to existing software. A key advance for the TIGER pipeline is the ability to analyze host and non-host sRNAs at genomic, parent RNA, and individual fragment levels. Results suggest that the majority of sRNAs on lipoproteins are derived from bacterial sources in the microbiome and environment. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of exRNA.
Project description:The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in evolutionary change. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. In the current study we explored variation between populations of Darwin’s finches living in adjacent “urban” and “rural” environments on Santa Cruz Island in the Galápagos. We tested for morphological, genetic, and epigenetic differences between the urban and rural populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find genetic differences between populations of either species, based on comparisons of copy number variation (CNV). In contrast, we did find epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially methylated regions (DMR), as well as their possible functional significance. In summary, our study documents local population epigenetic variation within species of Darwin’s finches.
Project description:Genomic DNA from 305 Col x Ct F2 individuals was extracted by CTAB and used to generate sequencing libraries as previously described (Hennig et al, 2018 G3). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3; Yelina et al, 2015 Genes & Dev).
Project description:Genomic DNA from 320 msh2 Col x Ct F2 individuals was extracted by CTAB and used to generate sequencing libraries as previously described (Hennig et al, 2018 G3). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3; Yelina et al, 2015 Genes & Dev).
Project description:Genomic DNA from 241 sni1-/- Col x Ct F2 individuals was extracted by CTAB and used to generate sequencing libraries as previously described (Hennig et al, 2018 G3). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3; Yelina et al, 2015 Genes & Dev).
Project description:Genomic DNA from 180 Col/Bur F2 individuals, and 186 taf4b/Bur F2 individuals, was extracted by CTAB and used to generate sequencing libraries as previously described (Ziolkowski et al, 2017 Genes & Dev). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3 (Bethesda); Yelina et al, 2015 Genes & Dev).
