RNAseq-based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae

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dc.contributor.authorMajeed, Aasim
dc.contributor.authorSingh, Amandeep
dc.contributor.authorChoudhary, Shurti
dc.contributor.authorBhardwaj, Pankaj
dc.date.accessioned2019-02-15T09:29:36Z
dc.date.accessioned2024-08-13T11:04:40Z
dc.date.available2019-02-15T09:29:36Z
dc.date.available2024-08-13T11:04:40Z
dc.date.issued2018
dc.description.abstractTaxaceae 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.en_US
dc.identifier.citationMajeed, Aasim., Singh, Amandeep., Choudhary, Shurti., Bhardwaj, Pankaj (2018) RNAseq?based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae. Cladistics. 35(1), 1-8. https://doi.org/10.1111/cla.12362en_US
dc.identifier.doi10.1111/cla.12362
dc.identifier.issnOnline-1096-0031
dc.identifier.urihttp://10.2.3.109/handle/32116/2000
dc.identifier.urlhttps://onlinelibrary.wiley.com/journal/10960031
dc.language.isoen_USen_US
dc.publisherWileyen_US
dc.subjectTaxaceae 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.en_US
dc.titleRNAseq-based phylogenetic reconstruction of Taxaceae and Cephalotaxaceaeen_US
dc.title.journalCladisticsen_US
dc.typeArticleen_US
dc.type.accesstypeOpen Accessen_US

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