Project description:In this study, we compared the transcriptome map of maize and sorghum using PacBio single-molecule long-read sequencing from multiple matched tissues in each species. Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the transcriptional profiles of both protein-coding and non-coding transcripts in matched tissues using large-scale single-molecule sequencing from 130 RSII cells and 5 Sequel cells, as well as deep short-read RNA sequencing. The use of multiple size-fractionated libraries (<1 kb, 12 kb, 23 kb, 35 kb, and >5 kb) enhanced our capture of non-redundant transcripts in these tissues.
Project description:In this study, using 2 glutinous sorghum and 2 non-glutinous sorghum as research objects, and their differences in grain appearance color, peel thickness, starch structure and small molecule metabolites were analyzed and compared. The results showed that the grain of 2 glutinous sorghum was red, and the grain of 2 non-glutinous sorghum was white. The thickness of pericarp (pericarp layer and seed layer) of glutinous sorghum (49.35-78.16 μm) was significantly higher than that of non-glutinous sorghum (33.39-49.03 μm) (P<0.05). The starch grains of glutinous sorghum were mainly oval-shaped and loosely arranged, while those in non-glutinous sorghum were irregular and tightly arranged. There were significant differences in the small molecule metabolites composition among different sorghum varieties. The marker metabolite of glutinous sorghum was catechin, while the marker metabolite of non-glutinous sorghum was 5-hydroxyindole-3-acetic acid. This study revealed significant differences in pericarp thickness, starch morphology, and small molecule metabolites between glutinous and non-glutinous sorghum, which was helpful to distinguish different sorghum varieties and lay a foundation for analyzing the relationship between liquor and grain.
Project description:Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the expression profiles of both protein-coding and non-coding transcripts in 11 matched tissues using single-molecule long-read and deep RNA sequencing. In this study, maize B73 line was planted at Cold Spring Harbor Laboratory upland farm, 11 tissues together with previously reported six tissues were collected, RNA was extracted, library was made and sequenced on the HiSeq 2500 PE125 platform at Woodbury Genome Center.
Project description:Examining RNA Transcript Changes in Stem Cells Undergoing Differentiation, Using Short and Long Reads Sequencing Technologies [Nanopore long reads]