The syntenic blocks used for constructing a synteny analysis map of the apple bHLH genes, as well as a comparison of apple and Arabidopsis bHLH genes, were obtained from the Plant Genome Duplication Database58, and the synteny diagrams were generated using Circos version 0.63 (http://circos.ca...
Gene duplication events occuring on different chromosomes were defined as segmental duplications47. The list of grape HB genes in duplicated genomic regions, and a comparison of grape and Arabidopsis genomes, were obtained from the Plant Genome Duplication Database72. Diagrams were generated using the...
as evidenced by the tight clustering in cladograms, (Figure1Band1C; Figure6). InArabidopsis,SROswere always present in pairs consistent with a previously proposed duplication event ([2,34], Plant Genome Duplication Databasehttp://chibba.agtec.uga.edu/duplication/index...
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164. Article PubMed PubMed Central Google Scholar Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware ...
2019). As of the end of 2022, the NCBI genome database (https://www.ncbi.nlm.nih.gov/genome/) includes 1028 reference genomes of varying depth and quality, which are published in various open-access repositories (including NCBI, Ensembl Plants, and Phytozome). The field of plant genomics...
(b) Proportion of orthologous genes in 12 plant genomes. (c) Estimation of the time of divergence (with error range shown in parentheses) of A. paniculata and 11 other species based on orthologous single-copy gene pairs. Stars highlight the location of whole-genome duplication (WGD) events....
Apricot is cultivated worldwide because of its high nutritive content and strong adaptability. Its flesh is delicious and has a unique and pleasant aroma. Apricot kernel is also consumed as nuts. The genome of apricot has been sequenced, and the transcri
RevisedandAcceptedOctober4,2005ABSTRACTGenomesthathavebeenhighlyconservedfollowing15increasesinploidy(byduplicationorhybridization)likeGlycinemax(soybean)presentchallengesduringgenomeanalysis.Athttp://soybeangenome.siu.edutheSoybeanGenomeDatabase(SoyGD)genomebrowserhas,since2002,integratedandservedthe20publiclyavailable...
Whole-genome duplication (WGD) is widespread in angiosperms and plays a crucial role in plant evolution and diversification [5,6]. Through WGD events, tandem repeats, transposable element-mediated repeats, and retrotransposon duplications, genomes can increase in size and gene number. This results in...
trichocarpa, tend to have multiple copies of trehalase genes via independent duplication events (Extended Data Fig. 8). We further compared the expression of trehalase genes in the mature plant bodies of P. guangdongensis and P. zijinensis using D. catenatum as a control and observed that the...