Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data

Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.

Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events.

The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

The hornwort genome and early land plant evolution

Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.

[The multiple regression analysis of related factors in chronic rhinosinusitis postoperative recurrence]

Objective: To study the relative factors of endoscopic surgical effect in chronic rhinosinusitis. Method:The study included 179 chronic rhinosinusitis patients in our hospital who had a nasal endoscopic surgery from January 2013 to June 2014, and evaluate the treatment effect one year after the surgery，the patients were divided into two groups :recurrent and non-recurrent. Collecting clinical data and using uni-variate and multivariate analysis to find out the risk factors of recurrence, then the regression equation was established. Result:There are 29 cases of recurrence and 150 cases of non-recurrent in the total 179 chronic rhinosinusitis patients with a nasal endoscopic surgery.Uni-variate analysis showed that smoking，nasal polyps, allergic rhinitis,bronchial asthma,deviation of nasal septum, gastro-esophageal reflux disease,scores of VAS,maxillary sinus integral ,anterior ethmoid sinus integral,posterior ethmoid sinus integral,sphenoid sinus integral,frontal sinus integral,ostiomeatal complex integral,total sinus integral were statistically significant between chronic rhinosinusitis recurrent group and non-recurrent group(P <0.05). Multivariate analysis showed that smoking,nasal polyps, allergic rhinitis, bronchial asthma, deviation of nasal septum,scores of VAS,anterior ethmoid sinus integral,sphenoid sinus integral, ostiomeatal complex integral, total sinus integral were statistically significant between chronic rhinosinusitis recurrent group and non-recurrent group(P <0.05). Among those factors, smoking,nasal polyps, allergic rhinitis ,scores of VAS ,anterior ethmoid sinus integral,sphenoid sinus integral are the strongest in difference. Conclusion:The effect of chronic rhinosinusitis endoscopic surgery is not only related to clinical typing ,but also closely related to smoking,nasal polyps , allergic rhinitis and their severity.

[Determination of relative elements of hard metal in workplace air and urine by inductive coupled plama]

Objective: To establish a rapid detection method regarding the air conditions of workplace and the workers' urine included Tungsten, Cobalt, Nickel, Titanium, Cadmium, Manganese, Lead and its compounds based on inductively coupled plasma mass spectrometry (ICP-MS) . Methods: The experiment adopts ICP-MS to deter-mine those metals in workshop air and workers urine, evaluate the detection's limitation, the precision and accuracy of the method. Using the membrane filter and urine freeze - dried metal standard material to verify this method. Results: Each element of correlation coefficient was greater than 0.999. The recovery rate of air samples was 91.6%~104.6%, within-batch RSD precision was 1.41%~3.50%, between-run precision was 1.28%~4.31%, urine samples recovery rate was 93.0%~102.6%, within - batch RSD precision was 1.25%~3.56%, between - run precision was 1.58%~4.67%, According to the method every element was within the scope of the standard reference, it was also showed that the established method is accurate and reliable. Conclusion: ICP-MS is an effective and feasible method to detect the workshop air and the workers' urine which included Tungsten, Cobalt, Nickel, Titanium, Cadmium, Manganese, Lead and its compounds.

[The clinical application of tinnitus handicap index(THI-12) Chinese version]

Objective:The original prospective of this study is to explore a convenient tinnitus severity assessment tool, using Chinese version of THI-12.Method:We surveyed 229 outpatients on their first hospital visits with primary tinnitus as chief complaint. Both the Chinese version THI-12 and the standard THI-25 were administrated. Their tinnitus grading and administration time were compared. The correlation between the two scores was evaluated. A reliability and factor analysis of the Chinese version of THI-12 was also performed.Result:Two hundred and fifteen of the 229 questionnaires were valid with a 93.9% response rate. The average administration time was(18.9±21.0) min for the standard THI-25 and(8.96±4.70)min for the Chinese version THI-12, which was significantly different. Pearson's correlation coefficient between the two total scores was r=0.833(P <0.01), which indicates a strong positive correlation.The tinnitus grading was not statistically significant(Z=-0.307，P >0.05).Cronbach's coefficient of THI-12 was α=0.765, suggesting good reliability and internal consistency. Factor analysis found three entries with characteristic values greater than 1. These three common factors explained 51.77% of the overall variance, suggesting that the 12 entries can be grouped into three dimensions(emotionality, sociality, concentration). Entry"Because of your tinnitus is it difficult for you to concentrate? "had the highest common value(0.78), suggesting that this entry would contribute the most should all entries be divided into three dimensions.Conclusion:The Chinese version THI-12 is time-efficient, has good reliability and internal structural validity, and provides good assessment of tinnitus severity.It can be widely applied in clinical practice.