Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

Abstract

BackgroundPhylogenetic relationship within different genera of Lemnoideae, a kind of small aquatic monocotyledonous plants, was not well resolved, using either morphological characters or traditional markers. Given that rich genetic information in chloroplast genome makes them particularly useful for phylogenetic studies, we used chloroplast genomes to clarify the phylogeny within Lemnoideae.MethodsDNAs were sequenced with next-generation sequencing. The duckweeds chloroplast genomes were indirectly filtered from the total DNA data, or directly obtained from chloroplast DNA data. To test the reliability of assembling the chloroplast genome based on the filtration of the total DNA, two methods were used to assemble the chloroplast genome of Landoltia punctata strain ZH0202. A phylogenetic tree was built on the basis of the whole chloroplast genome sequences using MrBayes v.3.2.6 and PhyML 3.0.ResultsEight complete duckweeds chloroplast genomes were assembled, with lengths ranging from 165,775 bp to 171,152 bp, and each contains 80 protein-coding sequences, four rRNAs, 30 tRNAs and two pseudogenes. The identity of L. punctata strain ZH0202 chloroplast genomes assembled through two methods was 100%, and their sequences and lengths were completely identical. The chloroplast genome comparison demonstrated that the differences in chloroplast genome sizes among the Lemnoideae primarily resulted from variation in non-coding regions, especially from repeat sequence variation. The phylogenetic analysis demonstrated that the different genera of Lemnoideae are derived from each other in the following order: Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia.DiscussionThis study demonstrates potential of whole chloroplast genome DNA as an effective option for phylogenetic studies of Lemnoideae. It also showed the possibility of using chloroplast DNA data to elucidate those phylogenies which were not yet solved well by traditional methods even in plants other than duckweeds.

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains

“…Our results are consistent with similar studies of the cotton genus ( Gossypium ), in which the length of LSC regions accounted for the cp genome size difference ( Chen et al, 2017 ). This is different from studies in duckweed species (Lemnoideae), in which differences in cp genome size were due to differences in IR regions ( Ding et al, 2017 ).…”

Duckweed (Lemnaceae): Its Molecular Taxonomy

“…However, the most evolved nature of the genus Wolffia could not yet be confirmed by molecular taxonomic tools. The phenetic tree structure of the plant family as reported by Les and Crawford (1999) and Les et al (2002) was recently confirmed by Ding et al (2017) using whole plastidic sequences of eight clones from all genera. However, the relative position of the genera Wolffiella vs. Wolffia in this tree cannot be defined because the branches representing these genera can be freely turned around the branching point.…”

“…With the advent of molecular taxonomic tools to the family of Lemnaceae, these three species were separated into two genera, Spirodela and Landoltia (changing the nomenclature of the species, Spirodela punctata to Landoltia punctata), based mainly on the investigation of the plastidic sequence rbcL (Les and Crawford, 1999). These results were confirmed by investigating the whole plastidic sequence analysis of Spirodela polyrhiza and Landoltia punctata (Ding et al, 2017). Taken together, there is no doubt that these three species should be organized into the two different genera as mentioned above.…”

Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes

“…The initial cp genomes were sequenced from tobacco and liverwort (Ohyama et al, 1986; Shinozaki et al, 1986). The plastid genome exhibits an overwhelming superiority for use in species discrimination of complex taxa and has been widely used to reveal their unresolved phylogenetics (Bayly et al, 2013; Du et al, 2017; Henriquez et al, 2014), such as in Araceae, Arundinarieae, Lemnoideae, Myrtaceae, Nelumbonaceae, Amborella , Nymphaea , Citrus , Gossypium and Oncidium (Bayly et al, 2013; Carbonell-Caballero et al, 2015; Ding et al, 2017; Goremykin et al, 2003; Goremykin et al, 2004; Henriquez et al, 2014; Li et al, 2014a; Ma et al, 2014; Wu et al, 2010; Xue et al, 2012). In a recent study, Park et al (2017) evaluated the relationships between F. ussuriensis and F. cirrhosa based on the chloroplast genome.…”