ColinearScan

[…] nodes., gene colinearity, reflecting shared ancestral gene order, is crucial to understand the genomic changes, especially in deconvoluting the evolution of complex plant genomes. by using colinearscan, we detected colinear genes within each cucurbit genome and between each pair of them (, online). grape genome was used as an outgroup reference to decipher the cucurbit genomes. […]

[…] respectively, to help distinguish homologies related to different events, recursive polyploidizations, and speciation., with the information on putative homologous genes as the input, we ran a colinearscan () to infer colinear relationships that would reveal homologous blocks within each genome and between genomes. synonymous nucleotide substitutions per synonymous site (ks) […]

[…] by running blastp among genes, we searched for potential anchors (e-value ≤ 1e-5; top five matches) between every possible pair of chromosomes within rice and pineapple, and between them. by running colinearscan (), we revealed homologous blocks within each genome and between different genomes (by setting maximal searching gap ≤ 50 genes and p-value < 0.05). by characterizing homologous […]

[…] search for potential anchors (e < 1e−10, top 5 matches) in the c. x clementina genome. afterwards, mcscan was employed to identify homologous regions. finally, syntenic blocks were evaluated by colinearscan. alignments with an e value < 1e−10 were considered as significant matches. the expression data of 371 c. sinensis genes were downloaded from cap and the correlation coefficients […]

[…] local server. then mcscan (multiple collinearity scan) [] was used to obtain the collinearity relation of each pair of species. the resulting collinearity chains were evaluated using a procedure in colinearscan and an e-value < 1e-10 was used as the cutoff., to examine the expression of pear genes, pear (pyrus bretschneideri) fruit samples at 15 d, 36 d, 80 d, 110 d, 145 d and 167 d […]