Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
Ann Bot. 2023 Feb 7;131(1):199-214. doi: 10.1093/aob/mcac062.
The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear.
New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan.
Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade.
Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
天南星科是单子叶植物中最多样化的科之一，具有许多形态和生态上的新颖性。质体和线粒体基因已被用于研究天南星科的系统发育，并解释其传粉生物学和生物地理学的转变。相比之下，全基因组复制（WGD）在八个亚科的进化中的作用尚不清楚。
通过 Illumina 测序生成了 65 种新的转录组或低深度全基因组序列。我们使用串联和种系树方法重建了天南星科的系统发育关系，然后使用 TreePL 估计了主要分支的年龄。我们通过 Ks 和基因树方法推断了 WGD 事件。我们通过时间依赖和性状依赖模型研究了多样化模式。使用 CAFE 和 InterProScan 分析了基因家族的扩张和功能富集。
Gymnostachydoideae 是最早分化的谱系，随后依次是 Orontioideae、Lemnoideae 和 Lasioideae。反过来，它们又被包含 Pothoideae 和 Monsteroideae 的“两性攀援植物”分支所跟随，该分支被解析为 Zamioculcadoideae 和 Aroideae 的单性花分支的姐妹。一个特殊的 WGD 事件 ψ（psi）发生在早白垩世，共同存在于真天南星科分支中。天南星科的净进化率随着时间的推移先下降后上升。在真天南星科分支的系统发育线上检测到了最佳的进化率转变，并且在 ψ-WGD 之后净进化率得到了增强。功能富集分析表明，一些基因，如热休克蛋白、糖苷水解酶和细胞色素 P450 的编码基因，在真天南星科分支中扩张。
我们的结果使用大量的单/低拷贝核基因，提高了对天南星科系统发育的理解。与 Proto-Araceae 组和 Lemnoideae 适应水生环境相反，我们对 WGD、多样化和功能富集的分析表明，WGD 可能在真天南星科分支适应热带、陆生环境的进化中发挥更重要的作用。这些见解为我们提供了新的资源来解释天南星科的进化。
