To further identify which one was the most likely candidate gene for CFW resistance, primers were designed to obtain both full length DNA and cDNA of the two genes from ten resistant cabbage inbred lines including the resistant parent (R_bulk) and ten susceptible lines including the susceptible parent (S_bulk) in order to conduct sequence alignment and mutation loci analysis (Table 4).
EJ participated in sequence acquisition and alignment, conducted phylogenetic analyses and drafted the MS. GG participated in DNA sequence acquisition and analyses.
Sequence quality assessment and alignment were conducted with CLC Genomics Workbench (version 5.0; CLC bio, Cambridge, MA, USA).
Sequence editing and alignment was conducted using CLC DNA Workbench 6.1 (CLC bio).
We selected nine unigenes that were respectively defined as mdPGRP (LE, SC), mdproPO1, mdPAP (1, 2, 3), and mdSerpin (3, 11) and conducted an alignment to their matched sequences in the RefSeq database of the M. domestica genome (Scott et al. 2014).
We developed scripts, which were used to remove 5' and 3' UTRs from the orthologous pairs and conduct a pairwise alignment in muscle 3.7 [ 103].
Filtering and alignment were then conducted on both libraries in CLC Genomics Workbench (version 5.0).
IMT carried out DNA and RNA gel blot analyses, screened BAC library, cloned GmNPR1 genes into a binary vector, transformed GmNPR1 genes into Arabidopsis, conducted sequence alignment and complementation analyses in Arabidopsis and, participated in drafting the initial manuscript and designing experiments.
KY carried out in vitro studies (cell culture and organ culture), participated in the design of the study, conducted sequence alignment and drafted the manuscript.
Additionally, we conducted simultaneous alignment and topology inference in a Bayesian framework using BAli-Phy for both the Apis and Solenopsis OBPs (AmOBPs; [4] and SiOBPs, respectively).
