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BACKGROUND: Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. This halophyte has enormous values for improving our understanding of salinity tolerance mechanisms. The genetic information of P. tenuiflora also is a potential resource that can be used for improving the salinity tolerance of cereals. RESULTS: Here, we sequenced and assembled the P. tenuiflora genome (2n = 14) through the combined strategy of Illumina, PacBio, and 10× genomic technique. We generated 43.2× PacBio long reads, 123.87× 10× genomic reads, and 312.6× Illumina reads. Finally, we assembled 2638 scaffolds with a total size of 1.107 Gb, contig N50 of 117 kb, and scaffold N50 of 950 kb. We predicted 39,725 protein-coding genes, and identified 692 tRNAs, 68 rRNAs, 702 snRNAs, 1376 microRNAs, and 691 Mb transposable elements. CONCLUSIONS: We deposited the genome sequence in NCBI and the Genome Warehouse in National Genomics Data Center. Our work may improve current understanding of plant salinity tolerance, and provides extensive genetic resources necessary for improving the salinity and drought tolerance of cereals.
Assuntos
Grão Comestível/genética , Genoma de Planta , Poaceae/genética , Tolerância ao Sal/genética , Plantas Tolerantes a Sal/genética , Mapeamento Cromossômico , Secas , Grão Comestível/fisiologia , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genômica , Proteínas de Plantas/genética , Poaceae/fisiologia , RNA não Traduzido/genética , Plantas Tolerantes a Sal/fisiologiaRESUMO
Background: Coronary microvascular dysfunction (CMD) assessed by the index of microcirculatory resistance (IMR) is associated with perioperative myocardial injury (PMI).The angiographically derived index of microcirculatory resistance (caIMR) represents a novel and accurate alternative to IMR. Objective: This study aims to evaluate the predictive ability of caIMR for PMI in patients with stable coronary artery disease (CAD) undergoing percutaneous coronary intervention (PCI). Methods: Consecutive patients with stable CAD undergoing elective PCI of a single lesion were recruited. caIMR was measured before and after revascularisation, and total creatine kinase-MB (CK-MB) and high-sensitivity troponin T (hsTnT) levels were measured before and within 24 h after PCI. Results: A total of 65 patients were enrolled and 26 patients fulfilled the diagnostic criteria for PMI. Post-PCI caIMR values were significantly higher in the PMI group than in the control group (27.02 ± 3.70 vs. 15.91 ± 3.43U, P < 0.001). Pearson correlation analysis showed that increased post-PCI caIMR values had a significant positive correlation with peak hsTnT (r = 0.803, P < 0.001) and peak CK-MB (r = 0.512, P = 0.001). Multivariate logistic regression analysis showed that post-PCI caIMR was an independent predictor of PMI (OR,1.731; 95 % CI:1.348-2.023; P < 0.001).ROC analysis suggested that the best cut-off value of post-PCI caIMR was 25.17U to diagnose PMI (AUC = 0.951, sensitivity 88.5 %, specificity 97.1 %). During a median follow-up 16 months, patients with PMI had a higher incidence of major adverse cardiovascular events (MACE) (42.31 % vs 5.13 %, P = 0.04). Conclusions: Post-PCI caIMR can accurately predict PMI and clinical outcomes in stable CAD patients undergoing elective PCI, which supports the use of caIMR in clinical practice.
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Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8â118.2) and 88.4 (77.7â102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.
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Dipterocarpaceae , Genômica , Floresta Úmida , Genoma , FilogeniaRESUMO
Dracaena, a remarkably long-lived and slowly maturing species of plant, is world famous for its ability to produce dragon's blood, a precious traditional medicine used by different cultures since ancient times. However, there is no detailed and high-quality genome available for this species at present; thus, the molecular mechanisms that underlie its important traits are largely unknown. These factors seriously limit the protection and regeneration of this rare and endangered plant resource. Here, we sequenced and assembled the genome of Dracaena cochinchinensis at the chromosome level. The D. cochinchinensis genome covers 1.21 Gb with a scaffold N50 of 50.06 Mb and encodes 31 619 predicted protein-coding genes. Analysis showed that D. cochinchinensis has undergone two whole-genome duplications and two bursts of long terminal repeat insertions. The expansion of two gene classes, cis-zeatin O-glucosyltransferase and small auxin upregulated RNA, were found to account for its longevity and slow growth. Two transcription factors (bHLH and MYB) were found to be core regulators of the flavonoid biosynthesis pathway, and reactive oxygen species were identified as the specific signaling molecules responsible for the injury-induced formation of dragon's blood. Our study provides high-quality genomic information relating to D. cochinchinensis and significant insight into the molecular mechanisms responsible for its longevity and formation of dragon's blood. These findings will facilitate resource protection and sustainable utilization of Dracaena.
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Croton , Dracaena , Dracaena/genética , Dracaena/metabolismo , Longevidade , Resinas Vegetais/metabolismo , Croton/genética , Croton/metabolismo , Cromossomos/metabolismoRESUMO
Halophytes and glycophytes exhibit clear differences in their tolerance to high levels of salinity. The genetic mechanisms underlying this differentiation, however, remain unclear. To unveil these mechanisms, we surveyed the evolution of salinity-tolerant gene families through comparative genomic analyses between the model halophyte Puccinellia tenuiflora and glycophytic Gramineae plants, and compared their transcriptional and physiological responses to salinity stress. Under salinity stress, the K+ concentration in the root was slightly enhanced in P. tenuiflora, but it was greatly reduced in the glycophytic Gramineae plants, which provided a physiological explanation for differences in salinity tolerance between P. tenuiflora and these glycophytes. Interestingly, several K+ uptake gene families from P. tenuiflora experienced family expansion and positive selection during evolutionary history. This gene family expansion and the elevated expression of K+ uptake genes accelerated K+ accumulation and decreased Na+ toxicity in P. tenuiflora roots under salinity stress. Positively selected P. tenuiflora K+ uptake genes may have evolved new functions that contributed to development of P. tenuiflora salinity tolerance. In addition, the expansion of the gene families involved in pentose phosphate pathway, sucrose biosynthesis, and flavonoid biosynthesis assisted the adaptation of P. tenuiflora to survival under high salinity conditions.
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The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of â¼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.
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Adaptação Fisiológica , Proteínas de Algas/genética , Chlamydomonas/fisiologia , Ambientes Extremos , Regulação da Expressão Gênica , Genoma , Transcriptoma , Proteínas de Algas/metabolismo , Regiões Antárticas , Chlamydomonas/genética , Camada de Gelo , Filogenia , Salinidade , Sequenciamento Completo do GenomaRESUMO
Spatholobus suberectus Dunn (S. suberectus), which belongs to the Leguminosae, is an important medicinal plant in China. Owing to its long growth cycle and increased use in human medicine, wild resources of S. suberectus have decreased rapidly and may be on the verge of extinction. De novo assembly of the whole S. suberectus genome provides us a critical potential resource towards biosynthesis of the main bioactive components and seed development regulation mechanism of this plant. Utilizing several sequencing technologies such as Illumina HiSeq X Ten, single-molecule real-time sequencing, 10x Genomics, as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), we assembled a chromosome-scale genome about 798 Mb in size. In total, 748 Mb (93.73%) of the contig sequences were anchored onto nine chromosomes with the longest scaffold being 103.57 Mb. Further annotation analyses predicted 31,634 protein-coding genes, of which 93.9% have been functionally annotated. All data generated in this study is available in public databases.