Triangle of U Fatty Acid Elongase (FAE1) Phylogenetic Tree

Alignment file and Newick tree for <em>Fatty Acid Elongase </em>(<em>FAE1</em>) orthologs among the Triangle of U species. <br> To investigate orthologs among the Triangle of U species, phylogenetic trees were constructed for three agriculturally important genes: <em>Flowering Locus C</em> (<em>FLC</em>), <em>Fatty Acyl Elongase 1</em> (<em>FAE1</em>) and <em>Fatty Acyl-CoA Reductase 1</em> (<em>FAR1</em>). 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.

本数据集包含芸薹属禹氏三角（Triangle of U）物种中脂肪酸延长酶（Fatty Acid Elongase，FAE1）同源基因的序列比对文件与Newick树文件。
为探究禹氏三角物种间的同源基因，我们针对3个具有重要农业应用价值的基因构建了系统发育树，分别为：开花位点C（Flowering Locus C，FLC）、脂酰延长酶1（Fatty Acyl Elongase 1，FAE1）以及脂酰辅酶A还原酶1（Fatty Acyl-CoA Reductase 1，FAR1）。
我们使用MUSCLE比对软件（Edgar, 2004）对编码序列与肽序列进行多重比对。
随后，依据蛋白质序列比对结果，通过PAL2NAL工具（Suyama等, 2006）对每组比对结果进行校正调整。
我们采用由所有比对序列组成的单一矩阵，基于贝叶斯信息准则（Bayesian Information Criterion, BIC），在IQ-TREE软件（Nguyen等, 2015）中筛选得到最优核苷酸替换模型。
最终，通过RAxML软件，采用GTR + CAT模型并设置1000次自展重复抽样，完成系统发育树的重构。