l e t t e r sBamboo represents the only major lineage of grasses that is native to forests and is one of the most important nontimber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between droughtresponsive and flowering genes.Bamboo is one of the most important non-timber forest products in the world. About 2.5 billion people depend economically on bamboo, and international trade in bamboo amounts to over 2.5 billion US dollars per year 1 . Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .Here, we report the draft genome of moso bamboo, a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area. Comparative genome-wide analyses of bamboo to other grass species, including rice, maize and sorghum, yielded new genetic insights into the rapid and marked phenotypic and ecological divergence of bamboo and closely related grasses.The moso bamboo genome contains 24 pairs of chromosomes 8 (2n = 48) and is characteristic of a diploid (Supplementary Fig. 1a). We conducted a flow cytometry analysis and estimated that it had a genome size of 2.075 Gb (2C = 4.24 pg; Supplementary Fig. 1b), which was very close to that estimated in a previous report 9 .Because it is difficult to generate an inbred line of moso bamboo, owing to its infrequent sexual reproduction and the long periods of time between flowering intervals, we selected five plants from a single individual rhizome of the moso bamboo ecotype (P. heterocycla var. pubescens) and performed whole-genome shotgun sequencing. We generated 295 Gb of raw sequence data (approximately 147-fold coverage), including Illumina short reads and 10,327 pairs of BAC end ...

BackgroundWith the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies.ResultsHere we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study.ConclusionAnalysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.

Previously, we have identified ZFAS1 as a potential new long non-coding RNA (lncRNA) biomarker of acute myocardial infarction (MI) and as a sarcoplasmic reticulum Ca2+-ATPase 2a (SERCA2a) inhibitor, causing intracellular Ca2+ overload and contractile dysfunction in a mouse model of MI. In the current study, we aimed to evaluate the effects of ZFAS1 on the apoptosis of cardiomyocytes in the MI mouse model. Knockdown of endogenous ZFAS1 by virus-mediated silencing shRNA or siZFAS1 partially abrogated the ischemia-induced apoptosis of cardiomyocytes. Overexpression of ZFAS1 in normal cardiomyocytes reduced the cell viability, similar to that observed in hypoxia-treated cardiomyocytes. Moreover, ZFAS1 cardiac-specific knock-in mice showed impaired cardiac function, adversely altered Ca2+ homeostasis, repressed expression and activities of SERCA2a, and increased apoptosis. At the subcellular level, ZFAS1 induced mitochondrial swelling and showed a pronounced decrease in mitochondrial membrane potential. At the molecular level, ZFAS1 activated the mitochondria apoptosis pathway, which could be nearly abolished by a calcium chelator. The effects of ZFAS1 were readily reversible upon knockdown of this lncRNA. Notably, ZFAS1-FD (only functional domain) mimicked the effects of full-length ZFAS1 in regulation of cardiomyocyte apoptosis. In conclusion, our study shows that ZFAS1, an endogenous SERCA2a inhibitor, induces mitochondria-mediated apoptosis via cytosolic Ca2+ overload. Therefore, anti-ZFAS1 might be considered a new therapeutic strategy for protecting cardiomyocytes from MI-induced apoptosis.

Cisplatin treatment some times leads to chemoresistance, which is now acknowledged partially due to the inductive expression of progesterone receptor membrane component (PGRMC)1 in ovarian cancer cells. PGRMC1 enhances autophagy, activates cytochrome p450, and inveigles signaling pathways to promote cell survival and reduce the effect of drug treatments. In this study, we give first line evidence that hyperoside inhibits cell viability, triggers autophagy and apoptosis in ovarian cancer cell lines. Mechanistically, PGRMC1-dependent autophagy was utilized by hyperoside to induce apoptotic cell death. Hyperoside induced the conversion of LC3B-I to LC3B-II and the formation of autophagosomes in ovarian cancer cells. Notably, PGRMC1 colocolized with LC3B‑II, and PGRMC1 overexpression enhanced hyperoside-induced autophagy and apoptosis, while PGRMC1 knockdown abrogated the action. Additionally, AKT signaling and Bcl-2 family were also involved in the hyperoside-induced autophagy and apoptosis. Importantly, in cisplatin-resistant ovarian cancer cells where PGRMC1 was overexpressed, hyperoside sensitized the cells to cisplatin treatment. Together these findings indicate hyperoside functions as a complementary therapy for ovarian cancer patients receiving platinum-based therapy.

DNA polymerases are responsible for ensuring stability of the genome and avoiding genotoxicity caused by a variety of factors during DNA replication. Consequently, these proteins have been associated with an increased cancer risk. DNA polymerase kappa (POLK) is a specialized DNA polymerase involved in translesion DNA synthesis (TLS) that allows DNA synthesis over the damaged DNA. Recently, some studies investigated relationships between POLK polymorphisms and cancer risk, but the role of POLK genetic variants in breast cancer (BC) remains to be defined. In this study, we aimed to evaluate the effects of POLK polymorphisms on BC risk.We used the Sequenom MassARRAY method to genotype 3 single nucleotide polymorphisms (SNPs) in POLK (rs3213801, rs10077427, and rs5744533), in order to determine the genotypes of 560 BC patients and 583 controls. The association of genotypes and BC was assessed by computing the odds ratio (OR) and 95% confidence intervals (95% CIs) from logistic regression analyses.We found a statistically significant difference between patient and control groups in the POLK rs10077427 genotypic groups, excluding the recessive model. A positive correlation was also found between positive progesterone receptor (PR) status, higher Ki67 index, and rs10077427 polymorphism. For rs5744533 polymorphism, the codominant, dominant, and allele models frequencies were significantly higher in BC patients compared to healthy controls. Furthermore, our results indicated that rs5744533 SNP has a protective role in the postmenopausal women. However, we failed to find any associations between rs3213801 polymorphism and susceptibility to BC.Our results indicate that POLK polymorphisms may influence the risk of developing BC, and, because of this, may serve as a prognostic biomarker among Chinese women.