Zhuang Yongbin, Tripp Erin A
Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA.
Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA.
DNA Res. 2017 Apr 1;24(2):179-192. doi: 10.1093/dnares/dsw054.
The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.
蓝花草属（野生矮牵牛；爵床科）的特点是在亲缘关系密切的物种中表现出极其多样的花形和花色。我们利用Illumina平台重建了美丽蓝花草的基因组草图，其支架大小为1021 Mb（约1.02 Gb），N50大小为17908 bp，覆盖了估计基因组（约1.1 Gb）的93%左右。该草图组装预测了40124个基因模型，对花青素颜色产生过程中涉及的四种关键酶[黄烷酮3-羟化酶（F3H）、类黄酮3'-羟化酶（F3'H）、类黄酮3'，5'-羟化酶（F3'5'H）和二氢黄酮醇4-还原酶（DFR）]进行的系统发育分析发现，这里采样的大多数被子植物都至少含有一份F3H、F3'H和DFR的拷贝。相比之下，不到一半（但包括美丽蓝花草）含有F3'5'H的拷贝，这支持了这样的观察结果，即这种酶所必需的蓝色花朵和/或果实在开花植物中不太常见。对美丽蓝花草中F3'H和DFR重复拷贝的Ka/Ks分析表明，前者存在纯化选择，但在后者中检测到了正选择的证据。美丽蓝花草的基因组序列和注释仅代表开花植物中大型且重要的菊分支中仅有的四个已测序科之一，因此，将有助于未来对这个多样化群体进行广泛的研究，特别是在花的进化方面。
