Low genetic variation is associated with low mutation rate in the giant duckweed.
ABSTRACT: Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.
Project description:Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively reproducing duckweed species, Lemna minor and Spirodela polyrhiza We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no substantial difference in mutation rate between mutation accumulation lines propagated under benign conditions and those grown under salt stress. Finally, we discuss the implications of interpreting mutation rate estimates in vegetatively propagating organisms.
Project description:Duckweed species <i>Lemna minor</i> and <i>Spirodela polyrhiza</i> are clonal plants with vegetative organs reduced to a frond and a root in <i>L. minor</i> or a frond and several roots in <i>S. polyrhiza</i>. They reproduce vegetatively by relatively rapid multiplication of their fronds. The habit of <i>S. polyrhiza</i> (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<sup>-2</sup> s<sup>-1</sup>) 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 <i>L. minor</i> and <i>S. polyrhiza</i>. <i>Spirodela polyrhiza</i> grew slower than <i>L. minor</i>, but both species grew fastest at medium light intensity (236 µmol m<sup>-2</sup> s<sup>-1</sup>). <i>Lemna minor</i> maintained the growth rates at high light intensity, while <i>S. polyrhiza</i> slowed down. <i>Spirodela polyrhiza</i> responded to deteriorating light conditions by increasing its frond surface area, thus optimising light capture. <i>Lemna minor</i> from the shady habitat enhanced light harvest by increasing chlorophyll <i>a</i> concentration, but did not invest more in frond enlargement than <i>L. minor</i> from the open habitat. Under shady conditions, <i>S. polyrhiza</i> is likely to achieve an advantage over <i>L. minor</i> due to the larger frond size of the former. Our findings suggest the existence of a trade-off between size and number in duckweed.
Project description:Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the monocot order Alismatales. They display the most rapid growth among flowering plants, vary?~?14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n?=?40; 160 Mbp/1C) and S. intermedia (2n?=?36; 160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S. intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both species' genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of a few new small chromosome rearrangements between both Spirodela species refined the karyotype and the chromosomal sequence assignment for S. intermedia.
Project description:Lipoxygenases (LOXs) (EC 22.214.171.124) catalyze the oxygenation of fatty acids and produce oxylipins, including the plant hormone jasmonic acid (JA) and its methyl ester, methyl jasmonate (MeJA). Little information is available about the LOX gene family in aquatic plants. We identified a novel LOX gene family comprising nine LOX genes in the aquatic plant <i>Spirodela polyrhiza</i> (greater duckweed). The reduced anatomy of <i>S. polyrhiza</i> did not lead to a reduction in LOX family genes. The 13-LOX subfamily, with seven genes, predominates, while the 9-LOX subfamily is reduced to two genes, an opposite trend from known LOX families of other plant species. As the 13-LOX subfamily is associated with the synthesis of JA/MeJA, its predominance in the Spirodela genome raises the possibility of a higher requirement for the hormone in the aquatic plant. JA-/MeJA-based feedback regulation during culture aging as well as the induction of LOX gene family members within 6 h of salt exposure are demonstrated.
Project description:We have undertaken an analysis of the inositol phosphates of Spirodela polyrhiza at a developmental stage when massive accumulation of InsP6 indicates that a large net synthesis is occurring. We have identified Ins3P, Ins(1,4)P2, Ins(3,4)P2 and possibly Ins(4,6)P2, Ins(3,4,6)P3, Ins(3,4,5,6)P4, Ins (1,3,4,5,6)P5, D- and/or L-Ins(1,2,4,5,6)P5 and InsP6 and revealed the likely presence of a second InsP3 with chromatographic properties similar to Ins(1,4,5)P3. The higher inositol phosphates identified show no obvious direct link to pathways of metabolism of second messengers purported to operate in higher plants, nor do they resemble the immediate products of plant phytase action on InsP6.
Project description:The aquatic monocotyledonous plant Spirodela polyrhiza was labelled with [33P]Pi for short periods under non-equilibrium conditions. An InsP6 fraction was obtained and dissected by using enantiospecific (enzymic) and non-enantiospecific (chemical) means to determine the relative labelling of individual phosphate substituents on the inositol ring of InsP6. Phosphates in positions D-1, -2, -3, -4, -5 and -6 contained approx. 21%, 32-39%, 9-10%, 14-16%, 19-23% and 16-18% of the label respectively. We conclude from the foregoing, together with identities [described in the preceding paper, Brearley and Hanke (1996) Biochem. J. 314, 215-225] of inositol phosphates found in this plant at a developmental stage associated with massive accumulation of InsP6, that synthesis of InsP6 from myo-inositol proceeds according to the sequence Ins3P-->Ins(3,4)P2-->Ins(3,4,6)P3-->Ins(3,4,5,6)P4-->Ins(1,3,4,5,6 ) P5-->InsP6 in Spirodela polyrhiza. These results represent the first description of the synthetic sequence to InsP6 in the plant kingdom and the only comprehensive description of endogenous inositol phosphates in any plant tissue. The sequence described differs from that reported in the slime mould Dictyostelium discoideum.
Project description:Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.
Project description:<h4>Main conclusion</h4> Identification of the polyamine biosynthetic pathway genes in duckweed S. polyrhiza reveals presence of prokaryotic as well as land plant-type ADC pathway but absence of ODC encoding genes. Their differential gene expression and transcript abundance is shown modulated by exogenous methyl jasmonate, salinity, and acidic pH. <h4>Abstract</h4> Genetic components encoding for polyamine (PA) biosynthetic pathway are known in several land plant species; however, little is known about them in aquatic plants. We utilized recently sequenced three duckweed (Spirodela polyrhiza) genome assemblies to map PA biosynthetic pathway genes in S. polyrhiza. PA biosynthesis in most higher plants except for Arabidopsis involves two pathways, via arginine decarboxylase (ADC) and ornithine decarboxylase (ODC). ADC-mediated PA biosynthetic pathway genes, namely, one arginase (SpARG1), two arginine decarboxylases (SpADC1, SpADC2), one agmatine iminohydrolase/deiminase (SpAIH), one N-carbamoyl putrescine amidase (SpCPA), three S-adenosylmethionine decarboxylases (SpSAMDc1, 2, 3), one spermidine synthase (SpSPDS1) and one spermine synthase (SpSPMS1) in S. polyrhiza genome were identified here. However, no locus was found for ODC pathway genes in this duckweed. Hidden Markov Model protein domain analysis established that SpADC1 is a prokaryotic/biodegradative type ADC and its molecular phylogenic classification fell in a separate prokaryotic origin ADC clade with SpADC2 as a biosynthetic type of arginine decarboxylase. However, thermospermine synthase (t-SPMS)/Aculis5 genes were not found present. Instead, one of the annotated SPDS may also function as SPMS, since it was found associated with the SPMS phylogenetic clade along with known SPMS genes. Moreover, we demonstrate that S. polyrhiza PA biosynthetic gene transcripts are differentially expressed in response to unfavorable conditions, such as exogenously added salt, methyl jasmonate, or acidic pH environment as well as in extreme temperature regimes. Thus, S. polyrhiza genome encodes for complete polyamine biosynthesis pathway and the genes are transcriptionally active in response to changing environmental conditions suggesting an important role of polyamines in this aquatic plant. <h4>Supplementary Information</h4> The online version contains supplementary material available at 10.1007/s00425-021-03755-5.
Project description:Background:The emollient properties of phthalates have led to their extensive production and intense use in plastic products. Owing to their weak covalent bonding with the plastic polymers, phthalates enter into the environment during their manufacturing, processing, disposal, consequently found their way directly into water sources, soil, and sediments. Methods:The present study envisaged the toxic effects of diethyl phthalate (DEP) on physiological and biochemical attributes of Spirodela polyrhiza, when exposed to various concentrations of DEP (0, 10, 20, 40, 80, 100, 200, and 400 ppm) for short term exposure period of seven days. Results:Plants of S. polyrhiza accumulated significant amount of DEP (112 mg kg-1 fw) when exposed to various concentrations of DEP for seven days. Results depicted that DEP toxicity significantly (p ? 0.05) affected growth parameters and pigments in treated S. polyrhiza as compared to control. Further, high doses of DEP (400 ppm) caused significant decrement in carbohydrate (86%), protein (76%) and elevation in MDA content (42%). Meanwhile, DEP altered the activities of antioxidant enzymes (SOD, CAT, APX, GPX and GR) along with the induction of enhanced levels of proline, electrolyte leakage and phenolic content. Scanning electron microscopic and confocal studies also confirmed oxidative stress in plants under DEP stress. Conclusions:Present findings will help understand the accumulation, tolerance, and detoxification mechanisms of DEP by S. polyrhiza to counteract the effects of reactive oxygen species (ROS), along with the evaluation of environmental threat for aquatic plants in aquatic ecosystems.
Project description:BACKGROUND:Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. RESULTS:In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling. CONCLUSIONS:This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.