Project description:The draft genome of L. sativa (lettuce) cv. Tizian was sequenced in two Illumina sequencing runs, mate pair and shotgun. This entry contains the RAW sequencing data.
Project description:Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). High temperature can induce earlier bolting which decreases in both quality and production of lettuce. However, knowledge underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems in the bolting period induced by high temperature (33 °C) compared with a control (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications. High temperature induced lettuce bolting, while control temperature did not. Of the 6656 proteins identified, 758 proteins significantly altered their expression level induced by high-temperature relative to the control, of which 409 were up-regulated and 349 down-regulated. Proteins with abundance level change were mainly involved in photosynthesis, carbohydrate metabolism, stress response, hormone synthesis, and signal transduction. These differential proteins were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involving in auxin (IAA) biosynthesis. Among the differentially expressed proteins associated with photosynthesis and tryptophan metabolism were up-regulated. Moreover, in gibberellin (GA) biosynthesis pathway, 10 of main enzymes of P450 were up-regulated. Proteins related to SAUR and GRP, implicated in IAA and GA signal transduction were up-regulated, and the phosphorylation and ubiquitination related proteins regulating IAA and GA signal transduction were also induced. These findings indicate that a high temperature enhances the function of photosynthesis, IAA and GA synthesis and signal transduction to promote the process of bolting, which is in line with the physiology and transcription levels of IAA and GA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivar of lettuce to restrain early bolting, which is vital for improving vegetable quality.
2019-11-12 | PXD008610 | Pride
Project description:Genetic Analysis of Colombian Sweetpotatoes Using a Genotyping Strategy based on Sequencing
Project description:We conducted two amiRNA (amiR417 and amiR519) transgenic lettuce lines. In order to confirm that the target artificial miRNAs (amiR417 and amiR519) were correctly transcribed and analysis the cleavage sites of the 3’ and 5’ ends of amiR471, small RNA fragments were extracted from ten independent positive T2 generations and examined using Solexa deep sequencing.
Project description:In this experiment we sequence the whole genome DNA of 28 unique populations of the root-knot nematode Meloidogyne hapla to investigate their genetic diversity using illumina sequencing. The hapla populations came from various locations, mostly in the Netherlands and Europe. The nematodes were maintained on tomato cv. Money Maker in the greenhouse of Wageningen University. After DNA extraction, DNA was sent for sequencing. The resulting sequence was used for calling variants and genetic analysis.
Project description:This study utilized the HIT-ISOseq method for high-throughput sequencing of RNA isoforms across multiple lettuce samples, generating millions of long reads per PacBio Sequel II SMRT Cell. Analysis of six tissue types revealed tissue-specific gene expression and RNA isoforms, facilitating updates to the lettuce reference genome annotation with expanded functional annotations.