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The chloroplast genome of the desiccation-tolerant moss Pseudocrossidium replicatum (Taylor) R.H. Zander.

ABSTRACT: Mosses in conjunction with hornworts and liverworts are collectively referred to as bryophytes. These seedless, nonvascular plants are the closest extant relatives of early terrestrial plants and their study is essential to understand the evolutionary first steps of land plants. Here we report the complete chloroplast (cp) genome sequence of Pseudocrossidium replicatum, a moss belonging to the Pottiaceae family that is common in the central highlands of Mexico, in South America, in southern USA, and in Kenia. The cp genome (plastome) of P. replicatum is 123,512 bp in size, comprising inverted repeats of 9,886 bp and single-copy regions of 85,146 bp (LSC) and 18,594 bp (SSC). The plastome encodes 82 different proteins, 31 different tRNAs, and 4 different rRNAs. Phylogenetic analysis using 16 cp protein-coding genes demonstrated that P. replicatum is closely related to Syntrichia ruralis, and the most basal mosses are Takakia lepidozioides followed by Sphagnum palustre. Our analysis indicates that during the evolution of the mosses' plastome, eight genes were lost. The complete plastome sequence reported here can be useful in evolutionary and population genetics.

SUBMITTER: Cevallos MA

PROVIDER: S-EPMC6726147 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSyntrichia caninervis is a desiccation-tolerant moss and the dominant bryophyte of the Biological Soil Crusts (BSCs) found in the Mojave and Gurbantunggut deserts. Next generation high throughput sequencing technologies offer an efficient and economic choice for characterizing non-model organism transcriptomes with little or no prior molecular information available.ResultsIn this study, we employed next generation, high-throughput, Illumina RNA-Seq to analyze the poly-(A)?+?mRNA from hydrated, dehydrating and desiccated S. caninervis gametophores. Approximately 58.0 million paired-end short reads were obtained and 92,240 unigenes were assembled with an average size of 493 bp, N50 value of 662 bp and a total size of 45.48 Mbp. Sequence similarity searches against five public databases (NR, Swiss-Prot, COSMOSS, KEGG and COG) found 54,125 unigenes (58.7%) with significant similarity to an existing sequence (E-value???1e-5) and could be annotated. Gene Ontology (GO) annotation assigned 24,183 unigenes to the three GO terms: Biological Process, Cellular Component or Molecular Function. GO comparison between P. patens and S. caninervis demonstrated similar sequence enrichment across all three GO categories. 29,370 deduced polypeptide sequences were assigned Pfam domain information and categorized into 4,212 Pfam domains/families. Using the PlantTFDB, 778 unigenes were predicted to be involved in the regulation of transcription and were classified into 49 transcription factor families. Annotated unigenes were mapped to the KEGG pathways and further annotated using MapMan. Comparative genomics revealed that 44% of protein families are shared in common by S. caninervis, P. patens and Arabidopsis thaliana and that 80% are shared by both moss species.ConclusionsThis study is one of the first comprehensive transcriptome analyses of the moss S. caninervis. Our data extends our knowledge of bryophyte transcriptomes, provides an insight to plants adapted to the arid regions of central Asia, and continues the development of S. caninervis as a model for understanding the molecular aspects of desiccation-tolerance.

Project description:BackgroundThe desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employed RNA-Seq and digital gene expression (DGE) technologies to study the genome-wide expression profiles of the dehydration and rehydration processes in this important desert plant.ResultsWe applied a two-step approach to investigate the gene expression profile upon rehydration in the moss Bryum argenteum using Illumina HiSeq2000 sequencing platform. First, a total of 57,247 transcript assembly contigs (TACs) were obtained from 54.79 million reads by de novo assembly, with an average length of 863 bp and N50 of 1,372 bp. Among the reconstructed TACs, 36,916 (64.5%) revealed similarity with existing protein sequences in the public databases. 23,509 and 21,607 TACs were assigned GO and KEGG annotation information, respectively. Second, samples were taken from 3 hydration stages: desiccated (Dry), rehydrated 2 h (R2) and rehydrated 24 h (R24), and DEG libraries were constructed for Differentially Expressed Genes (DEGs) discovery. 4,081 and 6,709 DEGs were identified in R2 and R24, compared with Dry, respectively. Compared to the desiccated sample, up-regulated genes after two hours of hydration are primarily related to stress responses. GO function enrichment network, EKGG metabolic pathway and MapMan analysis supports the idea of the rapid recovery of photosynthesis after 24 h of rehydration. We identified 770 transcription factors (TFs) which were classified into 50 TF families. 142 TF transcripts were up-regulated upon rehydration including 23 members of the ERF family.ConclusionsIn this study, we constructed a pioneering, high-quality reference transcriptome in B. argenteum and generated three DGE libraries to elucidate the changes of gene expression upon rehydration. Expression profiles consistent with the rapid recovery of photosynthesis (at R2) and the re-establishment of a positive carbon balance following rehydration (at R24) were observed. Our study will extend our knowledge of bryophyte transcriptomes and provide further insight into the molecular mechanisms related to rehydration and desiccation-tolerance.

Project description:Background and aimsThis study explores basic physiological features and time relations of recovery of photosynthetic activity and CO(2) uptake following rehydration of a desiccation-tolerant moss in relation to the full temporal sequence of cytological changes associated with recovery to the normal hydrated state. It seeks reconciliation of the apparently conflicting published physiological and cytological evidence on recovery from desiccation in bryophytes.MethodsObservations were made of water-stress responses and recovery using infrared gas analysis and modulated chlorophyll fluorescence, and of structural and ultrastructural changes by light and transmission electron microscopy.Key resultsNet CO(2) uptake fell to zero at approx. 40 % RWC, paralleling the fluorescence parameter PhiPSII at 200 micromol m(-2) s(-1) PPFD. On re-wetting the moss after 9-18 d desiccation, the initially negative net CO(2) uptake became positive 10-30 min after re-wetting, restoring a net carbon balance after approx. 0.3-1 h. The parameter F(v)/F(m) reached approx. 80 % of its pre-desiccation value within approx. 10 min of re-wetting. In the presence of the protein-synthesis inhibitors chloramphenicol and cycloheximide, recovery of F(v)/F(m) (and CO(2) exchange) proceeded normally in the dark, but declined rapidly in the light. Though initial recovery was rapid, both net CO(2) uptake and F(v)/F(m) required approx. 24 h to recover completely to pre-desiccation values. The fixation protocols produced neither swelling of tissues nor plasmolysis. Thylakoids, grana and mitochondrial cristae remained intact throughout the drying-re-wetting cycle, but there were striking changes in the form of the organelles, especially the chloroplasts, which had prominent lobes and lamellar extensions in the normally hydrated state, but rounded off when desiccated, returning slowly to their normal state within approx. 24 h of re-wetting. Sub-cellular events during desiccation and re-wetting were generally similar to those seen in published data from the pteridophyte Selaginella lepidophylla.ConclusionsInitial recovery of respiration and photosynthesis (as of protein synthesis) is very rapid, and independent of protein synthesis, suggesting physical reactivation of systems conserved intact through desiccation and rehydration, but full recovery takes approx. 24 h. This is consistent with the cytological evidence, which shows the thylakoids and cristae remaining intact through the whole course of dehydration and rehydration. Substantial and co-ordinated changes in other cell components, which must affect spatial relationships of organelles and metabolic systems, return to normal on a time span similar to full recovery of photosynthesis. Comparison of the present data with recently published results suggests a significant role for the cytoskeleton in desiccation responses.

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The chloroplast genome of the desiccation-tolerant moss Pseudocrossidium replicatum (Taylor) R.H. Zander.

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