Ogedengbe Joseph D, Ogedengbe Mosun E, Hafeez Mian A, Barta John R
Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada.
Parasitol Res. 2015 Nov;114(11):4149-60. doi: 10.1007/s00436-015-4646-1. Epub 2015 Aug 29.
Coccidia possess three distinct genomes: nuclear, mitochondrial, and plastid. Sequences from five genes located on these three genomes were used to reconstruct the phylogenetic relationships of members of the phylum Apicomplexa: 18S rDNA sequences from the nuclear (nu) genome, partial cytochrome c oxidase subunit I sequences from the mitochondrial (mt) genome, and partial 16S and 23S rDNA sequences and RNA polymerase B sequences from plastid (pl) genomes. Maximum parsimony, maximum likelihood, and Bayesian inference were used in conjunction with nuclear substitution models generated from data subsets in the analyses. Major groups within the Apicomplexa were well supported with the mitochondrial, nuclear, and a combination of mitochondrial, nuclear and concatenated plastid gene sequences. However, the genus Eimeria was paraphyletic in phylogenetic trees based on the nuclear gene. Analyses using the individual genes (18S rDNA and cytochrome c oxidase subunit I) resolved the various apicomplexan groups with high Bayesian posterior probabilities. The multi-gene, multi-genome analyses based on concatenated nu 18S rDNA, pl 16S, pl 23S, pl rPoB, pl rPoB1, and mt COI sequences appeared useful in resolving phylogenetic relationships within the phylum Apicomplexa. Genus-level relationships, or higher, appear best supported by 18S rDNA analyses, and species-level analyses are best investigated using mt COI sequences; for parasites for which both loci are available, nuclear 18S rDNA sequences combined with mitochondrial COI sequences provide a compact and informative molecular dataset for inferring the evolutionary relationships taxa in the Apicomplexa.
核基因组、线粒体基因组和质体基因组。来自这三种基因组上五个基因的序列被用于重建顶复门成员的系统发育关系：来自核（nu）基因组的18S rDNA序列、来自线粒体（mt）基因组的部分细胞色素c氧化酶亚基I序列，以及来自质体（pl）基因组的部分16S和23S rDNA序列和RNA聚合酶B序列。在分析中，最大简约法、最大似然法和贝叶斯推断与从数据子集生成的核替代模型结合使用。顶复门内的主要类群在基于线粒体、核以及线粒体、核和串联质体基因序列组合的系统发育树中得到了很好的支持。然而，基于核基因的系统发育树中艾美耳属是并系的。使用单个基因（18S rDNA和细胞色素c氧化酶亚基I）进行的分析以高贝叶斯后验概率解析了各种顶复门类群。基于串联的nu 18S rDNA、pl 16S、pl 23S、pl rPoB、pl rPoB1和mt COI序列的多基因、多基因组分析似乎有助于解析顶复门内的系统发育关系。属级及以上关系似乎通过18S rDNA分析得到的支持最好，而物种级分析最好使用mt COI序列进行研究；对于两个位点都可用的寄生虫，核18S rDNA序列与线粒体COI序列相结合，为推断顶复门中分类单元的进化关系提供了一个紧凑且信息丰富的分子数据集。
