期刊
MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 174, 期 -, 页码 -出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2022.107545
关键词
Chromosomal type; Phylotranscriptomics; Ranunculaceae; RNA-seq; Silica gel-dried leaf tissue
资金
- National Natural Science Founda-tion of China [31670207]
- Beijing Natural Science Foundation [5182016]
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. In this study, we tested whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies using Ranunculaceae. Our results showed that silica-dried samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms, leading to a higher resolution and statistical support in the resulting phylogeny.
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and down-loaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using these data, we conducted phylogenomic analyses, including concatenated-and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T-and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chro-mosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.
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