Abstract
Main conclusion
This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust molecular markers for phylogenetic inference.
Abstract
Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species: Spathiphyllum patulinervum, Stenospermation multiovulatum, Monstera adansonii, and Rhaphidophora amplissima. The quadripartite chloroplast genomes (size range 163,335–164,751 bp) consist of a pair of inverted repeats (25,270–25,931 bp), separating a small single copy region (21,448–22,346 bp) from a large single copy region (89,714–91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including psbK, ndhK, ndhD, rbcL, accD, rps8, and ycf2. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus Spathiphyllum and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.
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Acknowledgements
The authors would like to thank Dr. Barbara Schaal at Washington University in St. Louis and Dr. J. Chris Pires at the University of Columbia, Missouri for funding and laboratory support. The authors would also like to thank Dr. Tatiana Arias for valuable help in the laboratory and data processing. The authors also thank Emily Colletti in the aroid greenhouse at the Missouri Botanical Garden for help with living material.
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Funding for this study was provided by the GAANN fellowship, the Rettner B. Morris Scholarship, Washington University in St. Louis, J. Chris Pires Lab (NSF DEB 1146603).
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CH and TC collected plant samples and extracted total gDNA, constructed TruSeq libraries, and performed quality analyses of WGS short-read data. MC, AZ, and MM performed assembly and coverage depth analyses of all the genomes. A annotated all the genomes. A analysed all the genomes. A and IA interpreted data. A drafted the manuscript. A, IA, and CH edited the manuscript. A and IA designed and conceived research. IA and TC supervised the study.
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Data 2: Multiple alignment among Monsteroideae species used for the identification of suitable polymorphic regions (GENEIOUS 504 kb)
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Henriquez, C.L., Abdullah, Ahmed, I. et al. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). Planta 251, 72 (2020). https://doi.org/10.1007/s00425-020-03365-7
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DOI: https://doi.org/10.1007/s00425-020-03365-7