Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

中文翻译：

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Aldama（向日葵、菊科）36 个新叶绿体基因组序列中核苷酸多样性极低，以及与密切相关属的叶绿体基因组比较分析

Aldama（向日葵科、菊科）是向日葵科的一个多样化属。迄今为止，近 200 个菊科叶绿体基因组已被测序，但 Aldama 的质体仍未被描述。菊科植物的质体通常表现出很少的序列差异，因此，我们的假设是 Aldama 物种总体上是保守的。在这项研究中，我们新测序了 Aldama 的 36 个质体和属于其他 Heliantheae 属的 5 个物种（即 Dimerostemma asperatum、Helianthus tuberosus、Iostephaneheterophylla、Pappobolus lanatus var. lanatus 和 Tithonia diversifolia）作为外群。我们分析了组装的质体的结构和基因内容，并在 Aldama 和其他密切相关的属中进行了比较分析。正如预期的那样，阿尔达玛质体非常保守，所有研究物种的整体基因内容和方向都相似。质体的长度也是一致的，并且区域之间的连接处通常包含相同的基因并且具有相似的长度。与其他菊科物种类似，在所有组装的质体的大单拷贝（LSC）区域中检测到大~20 kb 和小~3 kb 倒置。核苷酸多样性非常低，127,466 bp 中只有 1,509 个可变位点（即，在 36 个 Aldama 质体比对中，除去其中一个 IR 后，1.18% 的位点是可变的）。只有一个基因 rbcL 显示出正选择的特征。与 Aldama 相比，所选外群的质体具有相似的基因内容和结构，并且在 LSC 区域也存在两个倒位。在基因 ycf2 中观察到不同长度的缺失。已为测序的 Aldama 和外群确定了多个 SSR。系统发育分析表明，由于墨西哥种 A. dentata 的位置，Aldama 不是单系的。所有巴西物种都形成了一个得到强有力支持的进化枝。我们的结果为物种水平上质体的进化和多样性带来了新的理解。