Majeed Aasim, Singh Amandeep, Choudhary Shruti, Bhardwaj Pankaj
Molecular Genetics Laboratory, Department of Plant Sciences, Central University of Punjab, Mansa Road, Bathinda, 151001, India.
Cladistics. 2019 Oct;35(5):461-468. doi: 10.1111/cla.12362. Epub 2018 Nov 29.
Taxaceae and Cephalotaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within Cephalotaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq-based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single-copy complete orthologous groups were selected for phylogenetic analysis. Maximum-likelihood, maximum-parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and Cephalotaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within Cephalotaxaceae.
红豆杉科和三尖杉科是两个具有重要经济价值的针叶树科。多年来，关于合并这两个科的问题一直存在很多争议。穗花杉属和榧属的分类地位也不明确。一些作者认为它们与红豆杉科关系更近，而另一些人则认为它们应归入三尖杉科。还有一些人则倾向于将它们提升为独立的族。不同的形态学、解剖学、胚胎学和系统发育学证据支持了其中一种观点，使得它们之间的精确划分仍未解决。在这里，我们使用基于RNA测序的方法，在选定的物种中获取直系同源基因，以重建这些科更可靠的系统发育。总共2.33123亿条原始 reads 进行了从头组装，为相应物种生成了9个不同的转录本组装。在9个物种的940191个组装转录本中，我们生成了409734个单基因，这些单基因被聚类到直系同源组中。总共选择了331个单拷贝完整直系同源组进行系统发育分析。最大似然法、最大简约法和贝叶斯系统发育树显示红豆杉科和三尖杉科为姐妹关系。我们的分析支持它们在科级水平上的独特性，也表明穗花杉属和榧属属于三尖杉科。
