Triangle of U Flowering Locus C (FLC) Phylogenetic Tree

Alignment file and Newick tree for Flowering Locus C (FLC) orthologs among the Triangle of U species.

To investigate orthologs among the Triangle of U species, phylogenetic trees were constructed for three agriculturally important genes: Flowering Locus C (FLC), Fatty Acyl Elongase 1 (FAE1) and Fatty Acyl-CoA Reductase 1 (FAR1). We aligned the coding sequences and peptide sequences using the MUSCLE alignment software (Edgar, 2004). Next, each alignment was adjusted using PAL2NAL (Suyama et al., 2006) according to the protein sequence alignments.  We used a single matrix comprised of the aligned sequences to determine the best-fit nucleotide substitution model under a Bayesian information criterion (BIC) in IQ-TREE (Nguyen et al., 2015). Lastly, the phylogenetic trees were reconstructed using RAxML under the GTR + CAT model with 1,000 bootstrap replicates.

本数据集包含十字花科U三角（Triangle of U）物种种间开花位点C（Flowering Locus C，FLC）同源基因的比对文件与Newick格式系统发育树。为探究U三角（Triangle of U）物种种间的同源基因，研究人员针对3个具有重要农业应用价值的基因——开花位点C（Flowering Locus C，FLC）、脂酰延长酶1（Fatty Acyl Elongase 1，FAE1）与脂酰-CoA还原酶1（Fatty Acyl-CoA Reductase 1，FAR1）构建系统发育树。首先使用MUSCLE序列比对软件（Edgar，2004）对各基因的编码序列与肽序列进行比对；随后依据蛋白质序列比对结果，通过PAL2NAL软件（Suyama等，2006）对每份序列比对结果进行校正。研究人员采用由所有比对序列组成的单矩阵，在IQ-TREE软件（Nguyen等，2015）中基于贝叶斯信息准则（Bayesian information criterion，BIC）确定最优核苷酸替换模型；最后使用RAxML软件以GTR + CAT模型并设置1000次自举重复，完成系统发育树的重构。