Abstract
BackgroundDuckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles.ResultsHere, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli.ConclusionsThe understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.
Highlights
Duckweeds (Lemnaceae) are aquatic plants distributed all over the world
Our trial confirmed that two pairs of repeats in the coding sequence of ycf2 gene were filled in the assembly of the chloroplast genome of S.polyrhiza
Here, a single circular strand genome with a size of 168, 956 bp is directly constructed by using a long-read assembly without any manual correction and sequence collapses, skipping further PCR amplification to fill unassembled gaps
Summary
Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. Lemnaceae (duckweeds) are the fastest growing plants including five genera of Spirodela, Landoltia, Lemna, Wolffiella and Wolffia. They are phylogenetically located at the early-diverging monocots of the Alismatale order. The chloroplast genome has dual characteristics of sequence variation and conservation, which are widely applied in the studies of population genetics and phylogenetic relationships. The entire chloroplast genomes show the potential to serve as a plant super-barcode to distinguish closely related species such as in Conyza (in the family of Asteraceae) [3, 4] and Theobroma cacao (in the family of Malvaceae) [5]. The chloroplast genome is one of the three genetic systems including nuclei, mitochondria, and plastids in plants that possesses both eukaryote-like introns and prokaryote-like operons [6]. The chloroplast is a vital organelle for plants, playing a crucial role by converting solar energy to carbohydrates through photosynthesis, and promoting their growth and starch accumulation
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