Guo Min, Zhou Qian, Zhou Yizhuang, Yang Linfeng, Liu Tianxiang, Yang Jinlong, Chen Yanling, Su Longxiang, Xu Jin, Chen Jing, Liu Feng, Chen Jiapeng, Dai Wenkui, Ni Peixiang, Fang Chengxiang, Yang Ruifu
Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China ; Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China ; BGI-Shenzhen, Shenzhen, China.
BGI-Shenzhen, Shenzhen, China.
PLoS One. 2014 Jan 29;9(1):e86752. doi: 10.1371/journal.pone.0086752. eCollection 2014.
The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.
浮霉菌科的物种是研究真核生物起源的理想类群。它们的细胞通过脂质胞内膜进行分裂，并且具有许多类似真核生物的分子特征。然而，它们的基因组结构、潜在能力和进化地位仍然未知。在本研究中，我们基于浮霉菌科的11个已测序物种寻找共同的蛋白质家族以及核心基因组/泛基因组。然后，我们基于它们的832个共同蛋白质家族构建了系统发育树。我们还使用直系同源簇数据库对这11个基因组进行了注释。此外，我们使用KEGG（京都基因与基因组百科全书）直系同源系统预测并重建了它们的核心/泛代谢途径。随后，我们在五个完整基因组中鉴定了基因组岛（GIs）和结构变异（SVs），并特别研究了两个浮霉菌科质粒在所有11个基因组中的整合情况。结果表明，浮霉菌科物种具有多样的基因组变异和独特的基因组特征，并且在人类应用方面具有巨大潜力。
