School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science, Jazan University, Saudi Arabia.
School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science and Technology, Vancouver Island University, British Columbia, Canada.
Mol Phylogenet Evol. 2019 Jul;136:76-86. doi: 10.1016/j.ympev.2019.04.001. Epub 2019 Apr 4.
Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
桉树 L'Hérit.（桃金娘科）是一个分类上复杂且高度特异的属，它主宰了澳大利亚大部分的木质植被。然而，关于某些群体的分子生物学和叶绿体多样性的信息非常有限，例如桉树分部 Adnataria，它存在于澳大利亚东部的许多林地生境中。我们报告了四个新的完整的桉树叶绿体基因组，其中三个基因组来自以前缺乏任何叶绿体参考序列的物种。使用从头开始的方法组装的 E. albens、E. conica、E. crebra 和 E. melliodora 的质体基因组彼此非常相似，在大小和结构上与之前发表的桉树叶绿体基因组相似。总共鉴定出 132 个基因（114 个单拷贝基因和 IR 区的 18 个重复基因），在基因顺序、内容和组织方面高度保守。通过比较基因组分析，发现基因间区的差异略有增加。使用参考指导方法组装了代表 12 个物种的 35 个额外个体的叶绿体序列。核苷酸取代率在蛋白质编码基因中有所不同，其中 17 个基因可能受到正选择，29 个基因不变。无论是整个重建的质体序列还是单个基因的系统发育分析，都与预期的物种边界或高级关系存在极端不匹配。质体关系比核 DNA 或分类关系更能通过地理预测，这表明基因流的影响远远超过不完全谱系分选的影响。这些结果为未来的研究提供了资源，并为桉树物种之间普遍存在的种间基因流提供了有价值的见解。
