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.
Highlights
Three kinds of genomes with different evolutionary origins and histories coexist in plant cells: nuclear, chloroplastic and mitochondrial
To test the reliability of assembling the cpDNA based on the filtration of the total DNA, the cpDNA of the same strain (L. punctata strain ZH0202) was assembled by using cp DNA directly
Together with four reported duckweeds cpDNAs, all of the duckweeds cpDNAs were within a range of 165,775 bp to 171,152 bp in length (Table 1), and carried two copies of IRs separated by a small single copy (SSC) and large single copy (LSC) (Fig. 2)
Summary
Three kinds of genomes with different evolutionary origins and histories coexist in plant cells: nuclear, chloroplastic and mitochondrial. Owing to the lower costs of next-generation sequencing (NGS), a new cost-effective method has arisen: indirectly assembling complete cpDNA by filtering from total DNA data (including DNA data of nuclei, cps and mitochondria) (Wang & Messing, 2011; Zhang et al, 2011). 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. This study demonstrates potential of whole chloroplast genome DNA as an effective option for phylogenetic studies of Lemnoideae. It 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
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