A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae.

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Date: Sept. 2022
Publisher: Elsevier B.V.
Document Type: Report
Length: 458 words

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Keywords Chromosomal type; Phylotranscriptomics; Ranunculaceae; RNA-seq; Silica gel-dried leaf tissue Highlights * Silica-dried plant tissues were successfully used for RNA-seq and phylotranscriptomic studies. * A well resolved and supported Ranunculaceae phylogeny was obtained. * The 11 tribes of the core Ranunculaceae grouped into two clades corresponding to the two major chromosome types. * WGDs were important, but not directly related to chromosome evolution in Ranunculaceae. Abstract 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 downloaded 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 chromosome 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. Author Affiliation: (a) School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China (b) Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA (c) Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China (d) Beijing Engineering Technology Research Center for Garden Plants, Beijing Forestry University Forest Science Co. Ltd., Beijing 100083, PR China * Corresponding authors at: 35# Eastern-Qinghua Rd., Beijing Forestry University, Beijing 100083, PR China (L. Xie). Article History: Received 20 August 2021; Revised 1 June 2022; Accepted 2 June 2022 (footnote)1 These authors contributed equally to this work. Byline: Jian He (a,1), Rudan Lyu (a,1), Yike Luo (a,1), Jiamin Xiao (a,1), Lei Xie [xielei@bjfu.edu.cn] (a,*), Jun Wen [wenj@si.edu] (b,*), Wenhe Li (a), Linying Pei (d), Jin Cheng (c)

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Gale Document Number: GALE|A708782309