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The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD. [ABSTRACT FROM AUTHOR]

The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD. [ABSTRACT FROM AUTHOR]

Background: Cerebral hyperperfusion syndrome (CHS) is a common complication after direct bypass surgery in patients with Moyamoya disease (MMD). Since preventive measures may be inadequate, we assessed whether the blood flow difference between the superficial temporal artery (STA) and recipient vessels (△BF) and the direct perfusion range (DPR) are related to CHS. Methods: We measured blood flow in the STA and recipient blood vessels before bypass surgery by transit-time probe to calculate △BF. Perfusion changes around the anastomosis before and after bypass were analyzed with FLOW800 to obtain DPR. Multiple factors, such as △BF, DPR, and postoperative CHS, were analyzed using binary logistic regression. Results: Forty-one patients with MMD who underwent direct bypass surgery were included in the study. Postoperative CHS symptoms occurred in 13/41 patients. △BF and DPR significantly differed between the CHS and non-CHS groups. The optimal receiver operating characteristic (ROC) curve cut-off value was 31.4 ml/min for ΔBF, and the area under the ROC curve (AUC) was 0.695 (sensitivity 0.846, specificity 0.500). The optimal cut-off value was 3.5 cm for DPR, and the AUC was 0.702 (sensitivity 0.615, specificity 0.750). Conclusion: Postoperative CHS is caused by multiple factors. △BF is a risk factor for CHS while DPR is a protective factor against CHS. [ABSTRACT FROM AUTHOR]

Background: Fibroblast Growth Factor 20 (FGF20)‐FGF receptor 1 (FGFR1) signaling is essential for cochlear hair cell (HC) and supporting cell (SC) differentiation. In other organ systems, FGFR1 signals through several intracellular pathways including MAPK (ERK), PI3K, phospholipase C ɣ (PLCɣ), and p38. Previous studies implicated MAPK and PI3K pathways in HC and SC development. We hypothesized that one or both would be important downstream mediators of FGF20‐FGFR1 signaling for HC differentiation. Results: By inhibiting pathways downstream of FGFR1 in cochlea explant cultures, we established that both MAPK and PI3K pathways are required for HC differentiation while PLCɣ and p38 pathways are not. Examining the canonical PI3K pathway, we found that while AKT is necessary for HC differentiation, it is not sufficient to rescue the Fgf20−/− phenotype. To determine whether PI3K functions downstream of FGF20, we inhibited Phosphatase and Tensin Homolog (PTEN) in Fgf20−/− explants. Overactivation of PI3K resulted in a partial rescue of the Fgf20−/− phenotype, demonstrating a requirement for PI3K downstream of FGF20. Consistent with a requirement for the MAPK pathway for FGF20‐regulated HC differentiation, we show that treating Fgf20−/− explants with FGF9 increased levels of dpERK. Conclusions: Together, these data provide evidence that both MAPK and PI3K are important downstream mediators of FGF20‐FGFR1 signaling during HC and SC differentiation. Key Findings: PI3K and MEK1/2 are necessary for hair cell differentiation while p38 and PLCγ are not.pAKT is necessary but not sufficient for hair cell differentiation.PTEN inhibition partially rescues Fgf20 knockout phenotype.dpERK is downstream of FGF20‐FGFR1 signaling. [ABSTRACT FROM AUTHOR]

SUMMARY: Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome‐wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome‐wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species. Significance Statement: Whole‐genome sequencing of Populus ilicifolia, a vulnerable and isolated poplar tree from the Tropics that can reproduce both sexually and asexually, was used to explore how population history and reproduction affected its genetic characteristics, genetic load, and its potential for tropical adaptation. [ABSTRACT FROM AUTHOR]

The whole chloroplast (cp) genome sequence of Camptotheca acuminata has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,382 bp in length, containing a large single copy region (LSC) of 89,493 bp and a small single copy region (SSC) of 16,540 bp, which were separated by two inverted repeat (IR) regions of 56,648 bp. The genome contained 129 genes, including 83 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall GC content of C. acuminata cp genome is 38%, while the corresponding values of the LSC, SSC and IR regions are 36.2, 32.7 and 42.3%, respectively. Further, phylogenetic analysis suggested that C. acuminata is closely related to the species of Davidia involucrata. [ABSTRACT FROM AUTHOR]

We characterized the chloroplast (cp) genome sequence of Banara guianensis by using Illumina pair-end sequencing platform, and the complete whole cp genome was 158,577 bp. That contains a large single copy region (LSC) of 85,863 bp and a small single copy region (SSC) of 17,334 bp, which were separated by a pair of 27,690 bp inverted repeat regions (IRs). The cp genome has 112 annotated genes, including 76 protein-coding genes and 36 tRNA genes. The overall GC content of it is 36.5%, while the corresponding values of the LSC, SSC and IR regions are 34.3, 30.2 and 42.0%, respectively. Furthermore, the phylogenetic analysis suggested that the location of B. guianensis is a sister of A. serrata and is an outgroup of other Salicaceae species. [ABSTRACT FROM AUTHOR]

DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. In this study, we examined single-base resolution methylomes of Populus euphratica under control and salt stress conditions using high-throughput bisulfite sequencing. Our data showed that the methylation levels of methylated cytosines in upstream 2 kb, downstream 2 kb, and repetitive sequences increased after salt treatment in leaves, but decreased in roots. We also found that heavy methylation in 100-bp upstream of the transcriptional start site repressed gene expression, while methylations within downstream 2 K and within the gene body were positively associated with gene expression. A total of 1893 and 1817 significant differentially methylated regions (DMRs) corresponding to 251 and 191 differentially methylated genes (DMGs) were identified in leaf and root tissues, respectively. These DMGs may play important roles in salt stress responses of P. euphratica through the changes of their DNA methylation levels. Overall, these findings provide valuable insights into our understanding of the interaction between gene expression and methylation of salt responses in poplars. [ABSTRACT FROM AUTHOR]