Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
Sci Rep. 2022 Jun 7;12(1):9375. doi: 10.1038/s41598-022-13449-x.
Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.
兰州百合（Baker）Boiss 是一种珍稀物种，具有宝贵的特性。然而，在揭示其遗传多样性和进化之前，其野生资源受到了威胁。此外，该属的系统发育关系仍存在一些模糊之处。因此，获得兰州百合的完整叶绿体序列及其与其他百合属物种的比较分析对于理解该属的进化以及遗传种群至关重要。进行了多尺度基因组水平的分析，特别是选择压力的分析。详细的第三代测序和分析揭示了一个完整的叶绿体基因组，大小为 151884bp，具有普通的四分体和受保护的结构，GC 含量为 37.0%。总的来说，在叶绿体基因组中鉴定出 113 个不同的基因，包括 30 个独特的 tRNA 基因、4 个独特的核糖体 RNA 基因和 79 个独特的蛋白质编码基因。这里鉴定出 3234 个 SSRs 和 2053 个复杂重复序列，并对 IR 扩张和收缩以及密码子使用偏好进行了全面分析。此外，全基因组滑动窗口分析表明，在 48 个百合 cp 基因组中，rpl32-trnL-ccsA、petD-rpoA、ycf1、psbI-trnS-trnG、rps15-ycf1、trnR、trnT-trnL 和 trnP-psaJ-rpl33 的变异性较高，在 SC 区域显示出较高的核苷酸变异性。在进行了 1128 次成对比较后，ndhB、psbJ、psbZ 和 ycf2 表现出零同义替换，显示出分化或遗传限制。此外，在 78 个蛋白质编码基因中，我们发现 accD 和 rpl36 受到正选择的影响：然而，在整个叶绿体蛋白质尺度上，百合物种经历了纯化选择。此外，重建了一个新的百合属系统发育树，我们认为百合属的分类比以前更加清晰。这里提供的遗传资源将有助于未来在物种鉴定、种群遗传学和百合属保护方面的研究。
