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Background  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. 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.    Results  Here, 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.    Conclusions  The 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.

bmc genomics

The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation