Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC6986005 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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

Zhang Yating Y An Dong D Li Changsheng C Zhao Zhixuan Z Wang Wenqin W

BMC genomics 20200128 1

<h4>Background</h4>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.<h4>Results</h4>Here, the complete chloroplast ge ...[more]

PMID: 31992185

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Project description:BackgroundAquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season.ResultsTo begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM) of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs). All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP) and allosteric activator (3-PGA) to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and APL3 were highly expressed in earlier stages of turion development, while APL1 expression was reduced throughout turion development.ConclusionsThese results suggest that the differential expression of APLs could be used to enhance energy flow from photosynthesis to storage of carbon in aquatic plants, making duckweeds a useful alternative biofuel feedstock.

Project description:Duckweed species Lemna minor and Spirodela polyrhiza are clonal plants with vegetative organs reduced to a frond and a root in L. minor or a frond and several roots in S. polyrhiza. They reproduce vegetatively by relatively rapid multiplication of their fronds. The habit of S. polyrhiza (large fronds with up to 21 roots) makes it a strong competitor among representatives of the family Lemnaceae, probably due to different resource-use strategies compared to small duckweed. In our study, light was the resource that affected the plants before and during the laboratory experiment. We sampled the plants from natural habitats differing in light conditions (open and shady) and grew them for 16 days in a thermostatic growth room at 22 °C under a 16:8 photoperiod and three light intensities (125, 236, 459 µmol photons m-2 s-1) to investigate the trade-off between frond enlargement and multiplication. Both species from the open habitat had higher growth rates based on the frond numbers and on surface area of fronds compared to plants from the shady habitat. They adopted different species-specific strategies in response to the experimental light conditions. The species size affected the growth rates in L. minor and S. polyrhiza. Spirodela polyrhiza grew slower than L. minor, but both species grew fastest at medium light intensity (236 µmol m-2 s-1). Lemna minor maintained the growth rates at high light intensity, while S. polyrhiza slowed down. Spirodela polyrhiza responded to deteriorating light conditions by increasing its frond surface area, thus optimising light capture. Lemna minor from the shady habitat enhanced light harvest by increasing chlorophyll a concentration, but did not invest more in frond enlargement than L. minor from the open habitat. Under shady conditions, S. polyrhiza is likely to achieve an advantage over L. minor due to the larger frond size of the former. Our findings suggest the existence of a trade-off between size and number in duckweed.

Dataset Information

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

Publications

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

Similar Datasets

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