Pipeline publication

[…] and USDA-NIFA, http://www.phytozome.net), and Cajanus cajan (Varshney et al., 2012) (project PRJNA72815, v1.0). L. angustifolius scaffolds carrying other CHI-fold protein sequences were subjected to the same procedure, however, genome sequences used for comparative mapping included also Arachis duranensis (accession V14167) and Arachis ipaensis (accession K30076) (Peanut Genome Project). The CoGe BLAST algorithm (Lyons et al., 2008) was used to perform sequence similarity analyses with the following parameters: e-value cut-off, 1e-20; word size, 8; gap existence cost, 5; gap elongation cost, 2; nucleotide match/mismatch scores, 1/-2. Microsyntenic blocks were visualized using the Web-based Genome Synteny Viewer (Revanna et al., 2011). The Synmap analysis tool was used (https://genomevolution.org/coge/SynMap.pl) to determine if identified syntenic loci were located in large conserved blocks of M. truncatula, L. japonicus, C. arietinum, G. max, P. vulgaris, and C. cajan genomes. Sequences were compared by the LAST (http://last.cbrc.jp/) algorithm. The DAGChainer algorithm was used to identify syntenic regions between genomes. The search was based on relative gene order, with the maximum distance between two matches set to 20 genes and the minimum number of aligned gene-pairs set to 5. To survey large scale macrosyntenic relationships, the sequences of molecular markers from linkage groups NLL-03 and NLL-15 from the genetic map (Kroc et al., 2014; Książkiewicz et al., 2015) were subjected to comparative mapping using the same legume genome sequences, bioinformatic tools and settings as those applied for scaffold analysis. The macrosyntenic relationships were inferred if at least four homology links from a particular L. angustifolius linkage group to […]

Pipeline specifications

Software tools GSV, SynMap, DAGchainer
Chemicals Heterocyclic Compounds, 2-Ring, Pyrans, Glycine