NCBI's Entrez system is an integrated search and retrieval system that provides access to a diverse set of 39 molecular and literature databases. Arabidopsis thaliana data is available in several NCBI resources ranging from primary data submissions, meta-data resources, and core resources that ...
Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a gl...
et al. A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc. Natl Acad. Sci. USA 102, 11934–11939 (2005). 27. Allen, T. M. et al. Uptake of liposomes by cultured mouse bone marrow macrophages: ...
thaliana (Additional file 1: Table S1). Thus, the emphasis of our investigation was on 37 SD-RLK genes. The gene and protein sequences of SD-RLKs were retrieved from the TAIR database (www. arabidopsis.org [31];). The physical location of these genes on A. thaliana genome was ...
The sequencing of the Arabidopsis thaliana genome (Arabidopsis Genome Initiative, 2000) offered the first opportunity to perform analyses on a plant organism’s entire compliment of P450s. The extent of P450 representation and diversity in A. thaliana exceeded expectations, eventually resulting in 272...
Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis tr...
thaliana database using Mascot 2.0. Mascot search parameters used with MS/MS data were: database = A. thaliana (nuclear, mitochondrial, and chloroplastic genome), enzyme = trypsin/proline, one missed cleavage allowed, peptide tolerance = 0.25 Da, MS/MS tolerance = 0.25 Da, peptide charge =...
[62]. Cleaned reads were mapped toArabidopsis thalianagenome assembly GCA_000001735.1 (TAIR10) using splice-aware aligner STAR [65], with mapping parameters adjusted toA. thalianagenome characteristics, basic two-pass mode, and allowing for 5% of mismatches to reference genome. Unique counts per ...
The demographic history ofA. thalianawas inferred using the MSMC model [28] based on two or four haploid genomes with default parameters. As theA. thalianaplant self-fertilizes, the genome of each strain can be considered as a haplotype sequence when heterozygous sites are excluded. Only homozyg...
thaliana genome assembly (TAIR10) revealed the presence of fragments from all Arabidopsis chromosomes, including fragments of the short and long arms (Chr1), complete centromeric repeat regions (Chr3 and Chr5) and telomeric regions (Chr2, Chr3, and Chr5) (pink and red zones in Fig. 1)....