Rono Peninah Cheptoo, Dong Xiang, Yang Jia-Xin, Mutie Fredrick Munyao, Oulo Millicent A, Malombe Itambo, Kirika Paul M, Hu Guang-Wan, Wang Qing-Feng
CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
Front Genet. 2020 Dec 9;11:560368. doi: 10.3389/fgene.2020.560368. eCollection 2020.
The genus L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of . The cp genomes of two African () species and were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in and , respectively. cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in and , respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in and , respectively. Significantly, the loss of group II intron in gene in species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in and 0.1418 in . The availability of complete cp genome in the genus will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.
L.属以其药用和观赏价值而闻名，广泛分布于全北区，在亚洲和非洲也有少数物种。由于杂交、自主无融合生殖和多倍体现象，L.属内物种的界定很困难，因此需要高效的基于分子的特征描述。在此，我们报告了L.属的初始完整叶绿体（cp）基因组。对两种非洲L.属物种进行了测序，并在蔷薇科中进行了系统发育和比较分析。这两个物种的cp基因组分别呈现出典型的环状四分体结构，长度分别为152,438和152,427碱基对（bp）。cp基因组由一对长度分别为25,923和25,915 bp的反向重复区域（IRa/IRb）组成，分别将17,980和17,981 bp的小单拷贝（SSC）区域与82,612和82,616 bp的大单拷贝（LSC）区域分开。cp基因组编码114个独特基因，包括88个蛋白质编码基因、37个转运RNA（tRNA）基因和4个核糖体RNA（rRNA）基因。此外，分别在两种物种中鉴定出88和95个简单序列重复（SSR）以及37和40个串联重复。值得注意的是，在某一物种的某一基因中检测到了II类内含子的缺失。基于26个完整cp基因组序列和27种蔷薇科物种的78个蛋白质编码基因序列的系统发育分析表明，L.属嵌套在蔷薇亚科内形成一个单系聚类。基于蛋白质编码区，检测到负选择压力（Ka/Ks < 1），某一物种的平均Ka/Ks值为0.1322，另一物种为0.1418。L.属完整cp基因组的可得性将有助于蔷薇科的物种界定以及进一步的系统发育和进化研究。
