The evolution of Gnetales is ambiguous, and their phylogenetic position is still debated. The biological and molecular processes may evolve with the evolutionary history of a species or a clade. The molecular/biological processes of phylogenetically similar lineages closely follow their evolutionary pattern. If Gnetales evolved as a sister to Pinaceae, cupressophytes or Coniferales as a whole, then it is expected that the molecular or biological processes may reflect this pattern of evolution. In light of this, we deciphered the codon usage pattern of Gnetales, compared it with angiosperms, Pinaceae, cupressophytes and Coniferales as a whole. We evaluated whether this important molecular process has evolved in agreement with the Anthophyte, Gnepine, Gnecup or Gnetifer hypothesis. We observed that Gnetales prefer A/U-ending codons to G/C-ending codons like other lineages. Natural selection plays a dominant role in governing the codon usage bias (CUB). The CpA/CpT dinucleotides were over-represented, whereas the CpG dinucleotide was suppressed. Hierarchical clustering (HC) and correspondence analysis (CA) on relative synonymous codon usage values of 59 synonymous codons showed Gnetales as a sister clade to Coniferales as a whole and revealed that the codon usage pattern in Gnetales has evolved in close accordance with the Gnetifer hypothesis.

中文翻译：

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Gnetales 的密码子使用模式与 Gnetifer 假说密切相关

Gnetales 的进化是模棱两可的，它们的系统发育位置仍然存在争议。生物和分子过程可能随着物种或进化枝的进化史而进化。系统发育相似谱系的分子/生物学过程密切遵循它们的进化模式。如果 Gnetales 作为一个整体进化为松科、铜植物或针叶树的姐妹，那么预计分子或生物过程可能反映这种进化模式。有鉴于此，我们破译了Gnetales的密码子使用模式，并将其与被子植物、松科、铜植物和松柏科作为一个整体进行了比较。我们评估了这一重要分子过程的进化是否与 Anthophyte、Gnepine、Gnecup 或 Gnetifer 假说一致。我们观察到与其他谱系一样，Gnetales 更喜欢 A/U 结尾的密码子而不是 G/C 结尾的密码子。自然选择在控制密码子使用偏差 (CUB) 中起主导作用。CpA/CpT 二核苷酸过多，而 CpG 二核苷酸被抑制。对 59 个同义密码子的相对同义密码子使用值的层次聚类 (HC) 和对应分析 (CA) 表明，Gnetales 是整个 Coniferales 的姐妹进化枝，并揭示了 Gnetales 中的密码子使用模式已与 Gnetifer 假设密切相关.