The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

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The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Mungbean (Vigna radiate L. Wilczek) is an important legume crop for its valuable nutritional and health benefits. Desiccation tolerance is a capacity of seeds to survive and maintain physiological activities during storage and under stress conditions. Many studies of desiccation tolerance have been reported in other legume crop, such as soybean and Medicago truncatula with little studies in the mungbean. In this study, the transcript profiles of mungbean seeds under different imbibition times were investigated for desiccation tolerance using RNA-sequencing (RNA-seq). A total of 3,210 differentially expressed genes (DEGs) were found at the key period of desiccation tolerance (3h to 18h of imbibition). GO and KEGG analysis showed that ‘response to stimulus’, ‘transcription regulator’, ‘methylation’ and ‘starch and sucrose metabolism’ were enriched for desiccation tolerance. Clustering analysis also showed that many transcription factors (MYB, AP2, and NAC), HSPs, embryogenesis abundant (LEA) proteins, and genes encoding methyltransferase and histone were differentially expressed. Nine of these DEGs were further validated by quantitative RT-PCR (qRT-PCR). Our study extends our knowledge of mungbean transcriptomes and further provides insight into the molecular mechanism of desiccation tolerance as well as new strategies for developing drought-tolerant crops.

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Transcriptomic Profiling Reveals Metabolic and Regulatory Pathways in the Desiccation Tolerance of Mungbean (Vigna radiata [L.] R. Wilczek)

One of the most extreme environments on our planet is the Maritime Antarctic territory, due to its low-water availability, which restricts the development of plants. Sanionia uncinata Hedw. (Amblystegiaceae), the main colonizer of the Maritime Antarctic, has effective mechanisms to tolerate this environment. It has been described that the tolerance to desiccation is mediated by the hormone abscisic acid (ABA), antioxidants systems, accumulation of compatible solutes and proteins of the late embryogenesis abundant (LEA). However, to date, these mechanisms have not been described in S. uncinata. Therefore, in this work, we postulate that the tolerance to desiccation in the Antarctic moss S. uncinata is mediated by the accumulation of ABA, the osmolytes proline and glycine betaine, and dehydrins (an LEA class 11 proteins). To demonstrate our hypothesis, S. uncinata was subjected to desiccation for 24 h (loss in 95% of water content), and the effects on its physiological, photosynthetic, antioxidant and biochemical parameters were determined. Our results showed an accumulation of ABA in response to water loss, and the activation of protective responses that involves an increment in levels of proline and glycine betaine, an increment in the activity of antioxidant enzymes such as SOD, CAT, APX and POD, and the accumulation of dehydrins proteins. The results showed, suggest that S. uncinata is a  desiccation-tolerant moss, property mediated by high cellular plasticity regulated by ABA.

/pdf/desiccation-tolerance-in-the-antarctic-moss-sanionia-4e2h3dzh40.pdf

Desiccation tolerance in the Antarctic moss Sanionia uncinata

Bryophytes are small land plants that have many morphological and physiological features different from vascular plants. With distinct water relations of bryophytes, many bryophyte species exhibit high degrees of tolerance to freezing and desiccation. The tolerance is sustained by the constitutive repair mechanism and the inducible mechanism regulated by environmental signals that provoke specific responses within the cells. Bryophyte cells sense changes in environmental conditions such as decreases in osmotic potential and temperature and that some responses are likely to be mediated by the stress hormone, abscisic acid. Due to their simple structures and high degrees of dehydration tolerance, bryophytes are useful for physiological studies on abiotic stress response and also for analysis of signal sensing and transduction of environmental signals. Furthermore, the basal phylogenetic position of bryophytes in land plants provides many insights into the evolutionary events for conquest of land by the ancestors of plants and subsequent diversification of species as well as their survival strategies in the terrestrial environment.

Mechanisms Underlying Freezing and Desiccation Tolerance in Bryophytes.

Liverwort Marchantia polymorpha is considered as the key species for addressing a myriad of questions in plant biology. Exploration of drought tolerance mechanism(s) in this group of land plants offers a platform to identify the early adaptive mechanisms involved in drought tolerance. The current study aimed at elucidating the drought acclimation mechanisms in liverwort's model M. polymorpha. The gemmae, asexual reproductive units of M. polymorpha, were exposed to sucrose (0.2 M), mannitol (0.5 M) and polyethylene glycol (PEG, 10%) for inducing physiological drought to investigate their effects at morphological, physiological and biochemical levels. Our results showed that drought exposure led to extreme growth inhibition, disruption of membrane stability and reduction in photosynthetic pigment contents in M. polymorpha. The increased accumulation of hydrogen peroxide and malondialdehyde, and the rate of electrolyte leakage in the gemmalings of M. polymorpha indicated an evidence of drought-caused oxidative stress. The gemmalings showed significant induction of the activities of key antioxidant enzymes, including superoxide dismutase, catalase, ascorbate peroxidase, dehydroascorbate reductase and glutathione S-transferase, and total antioxidant activity in response to increased oxidative stress under drought. Importantly, to counteract the drought effects, the gemmalings also accumulated a significant amount of proline, which coincided with the evolutionary presence of proline biosynthesis gene Δ1-pyrroline-5-carboxylate synthase 1 (P5CS1) in land plants. Furthermore, the application of exogenous abscisic acid (ABA) reduced drought-induced tissue damage and improved the activities of antioxidant enzymes and accumulation of proline, implying an archetypal role of this phytohormone in M. polymorpha for drought tolerance. We conclude that physiological drought tolerance mechanisms governed by the cellular antioxidants, proline and ABA were adopted in liverwort M. polymorpha, and that these findings have important implications in aiding our understanding of osmotic stress acclimation processes in land plants.

Acclimation of liverwort Marchantia polymorpha to physiological drought reveals important roles of antioxidant enzymes, proline and abscisic acid in land plant adaptation to osmotic stress.

Drought is an increasingly important limitation on plant productivity worldwide. Understanding the mechanisms of drought tolerance in plants can lead to new strategies for developing drought-tolerant crops. Many moss species are able to survive desiccation—a more severe state of dehydration than drought. Research into the mechanisms and evolution of desiccation tolerance in basal land plants is of particular significance to both biology and agriculture. In this study, we conducted morphological, cytological, and physiological analyses of gametophytes of the highly desiccation-tolerant bryophyte Atrichumundulatum (Hedw.) P. Beauv during dehydration and rehydration. Our results suggested that the mechanisms underlying the dehydration–recovery cycle in A. undulatum gametophytes include maintenance of membrane stability, cellular structure protection, prevention of reactive oxygen species (ROS) generation, elimination of ROS, protection against ROS-induced damage, and repair of ROS-induced damage. Our data also indicate that this dehydration–recovery cycle consists not only of the physical removal and addition of water, but also involves a highly organized series of cytological, physiological, and biochemical changes. These attributes are similar to those reported for other drought- and desiccation-tolerant plant species. Our findings provide major insights into the mechanisms of dehydration-tolerance in the moss A. undulatum.

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Dehydration-responsive features of Atrichum undulatum.

Mitochondrial genomes (mitogenomes) are involved in cellular energy metabolism and have been shown to undergo adaptive evolution in organisms with increased energy-consuming activities. The genetically selected high royal jelly-producing bees (RJBs, Apis mellifera ligustica) in China can produce 10 times more royal jelly, a highly nutritional and functional food, relative to unselected Italian bees (ITBs). To test for potential adaptive evolution of RJB mitochondrial genes, we sequenced mitogenomes from 100 RJBs and 30 ITBs. Haplotype network and phylogenetic analysis indicate that RJBs and ITBs are not reciprocally monophyletic but mainly divided into the RJB- and ITB-dominant sublineages. The RJB-dominant sublineage proportion is 6-fold higher in RJBs (84/100) than in ITBs (4/30), which is mainly attributable to genetic drift rather than positive selection. The RJB-dominant sublineage exhibits a low genetic diversity due to purifying selection. Moreover, mitogenome abundance is not significantly different between RJBs and ITBs, thereby rejecting the association between mitogenome copy number and royal jelly-producing performance. Our findings demonstrate low genetic diversity levels of RJB mitogenomes and reveal genetic drift and purifying selection as potential forces driving RJB mitogenome evolution.

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Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica)

Tissue phenotypic plasticity facilitates rapid adaptation of organisms to biotic and/or abiotic pressure. The reproductive capacity of honey bee workers (Apis mellifera) is plastic and responsive to pheromones produced by broods and the queen. Egg laying workers (ELWs), which could reactivate their ovaries and lay haploid eggs upon queen lost, have been commonly discussed from many aspects. However, it remains unclear whether midgut homeostasis in ELWs is affected during plastic changes. Here, we found that the expression of nutrition- and autophagy-related genes was up-regulated in the midguts of ELWs, compared with that in nurse workers (NWs) by RNA-sequencing. Furthermore, the area and number of autophagosomes were increased, along with significantly increased cell death in the midguts of ELWs. Moreover, cell cycle progression in the midguts of ELWs was increased compared with that in NWs. Consistent with the up-regulation of nutrition-related genes, the body and midgut sizes, and the number of intestinal proliferation cells of larvae reared with royal jelly (RJ) obviously increased more than those reared without RJ in vitro. Finally, cell proliferation was dramatically suppressed in the midguts of ELWs when autophagy was inhibited. Altogether, our data suggested that autophagy was induced and required to sustain cell proliferation in ELWs’ midguts, thereby revealing the critical role of autophagy played in the intestines during phenotypic plasticity changes.

/pdf/autophagy-is-required-to-sustain-increased-intestinal-cell-1o82v4iy.pdf

Autophagy Is Required to Sustain Increased Intestinal Cell Proliferation during Phenotypic Plasticity Changes in Honey Bee (Apis mellifera)

Abstract Nitric oxide (NO) is a key player in numerous physiological processes. Excessive NO induces DNA damage, but how plants respond to this damage remains unclear. We screened and identified an Arabidopsis NO hypersensitive mutant and found it to be allelic to TEBICHI/POLQ, encoding DNA polymerase θ. The teb mutant plants were preferentially sensitive to NO- and its derivative peroxynitrite-induced DNA damage and subsequent double-strand breaks (DSBs). Inactivation of TEB caused the accumulation of spontaneous DSBs largely attributed to endogenous NO and was synergistic to DSB repair pathway mutations with respect to growth. These effects were manifested in the presence of NO-inducing agents and relieved by NO scavengers. NO induced G2/M cell cycle arrest in the teb mutant, indicative of stalled replication forks. Genetic analyses indicate that Polθ is required for translesion DNA synthesis across NO-induced lesions, but not oxidation-induced lesions. Whole-genome sequencing revealed that Polθ bypasses NO-induced base adducts in an error-free manner and generates mutations characteristic of Polθ-mediated end joining. Our experimental data collectively suggests that Polθ plays dual roles in protecting plants from NO-induced DNA damage. Since Polθ is conserved in higher eukaryotes, mammalian Polθ may also be required for balancing NO physiological signaling and genotoxicity.

Ruoyang Hu

Papers

Dehydration-responsive features of Atrichum undulatum.

Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica)

Autophagy Is Required to Sustain Increased Intestinal Cell Proliferation during Phenotypic Plasticity Changes in Honey Bee (Apis mellifera)

TEB/POLQ plays dual roles in protecting Arabidopsis from NO-induced DNA damage