Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana.

Short interfering RNAs (siRNAs) homologous to transcriptional regulatory regions can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) of target genes. In our system, siRNAs are produced by transcribing an inverted DNA repeat (IR) of enhancer sequences, yielding a hairpin RNA that is processed by several Dicer activities into siRNAs of 21-24 nt. Primarily 24-nt siRNAs trigger RdDM of the target enhancer in trans and TGS of a downstream GFP reporter gene. We analyzed siRNA accumulation from two different structural forms of a trans-silencer locus in which tandem repeats are embedded in the enhancer IR and distinguished distinct RNA polymerase II (Pol II)- and Pol IV-dependent pathways of siRNA biogenesis. At the original silencer locus, Pol-II transcription of the IR from a 35S promoter produces a hairpin RNA that is diced into abundant siRNAs of 21-24 nt. A silencer variant lacking the 35S promoter revealed a normally masked Pol IV-dependent pathway that produces low levels of 24-nt siRNAs from the tandem repeats. Both pathways operate concurrently at the original silencer locus. siRNAs accrue only from specific regions of the enhancer and embedded tandem repeat. Analysis of these sequences and endogenous tandem repeats producing siRNAs revealed the preferential accumulation of siRNAs at GC-rich regions containing methylated CG dinucleotides. In addition to supporting a correlation between base composition, DNA methylation and siRNA accumulation, our results highlight the complexity of siRNA biogenesis at repetitive loci and show that Pol II and Pol IV use different promoters to transcribe the same template.

Electrophysiological Effects of Dexmedetomidine on Sinoatrial Nodes of Rabbits.

BACKGROUND: The purpose of this study was to investigate the electrophysiological effects of dexmedetomidine on pacemaker cells in sinoatrial nodes of rabbits. METHODS: Healthy rabbits were anesthetized intravenously with sodium pentobarbital, and the hearts were quickly dissected and mounted in a tissue bath. Machine-pulled glass capillary microelectrodes which were connected to a high input impedance amplifier and impaled in dominant pacemaker cells. Thereafter, an intracellular microelectrode technique was used to record action potential. RESULTS: The amplitude of action potential, velocity of diastolic (phase 4) depolarization, and rate of pacemaker firing in normal pacemaker cells in sinoatrial node were decreased by use of dexmedetomidine (0.5 ng/ml, 5 ng/ml, 50 ng/ml) in a concentration-dependent manner. Pretreatment with yohimbine (1 µM), did not alter the effects of dexmedetomidine (5 ng/ml) on sinoatrial node pacemaker cells. Pretreatment with CsCl (2 mmol/L), dexmedetomidine (5 ng/ml) decreased the amplitude of action potential, but had no significant effect on other parameters of action potential. CONCLUSIONS: Dexmedetomidine exerts inhibitory electrophysiological effects on pacemaker cells in sinoatrial nodes of rabbits in a concentration-dependent manner, which may not be mediated by alpha 2-adrenoreceptor. KEY WORDS: Action potential; Cardiology; Dexmedetomidine; Pacemaker activity; Sinoatrial node.

Poleward migration of tropical corals inhibited by future trends of seawater temperature and calcium carbonate (CaCO3) saturation.

Poleward range expansion of marine organisms is commonly attributed to anthropogenic ocean warming. However, the extent to which a single species can migrate poleward remains unclear. In this study, we used molecular data to examine the current distribution of the Pocillopora damicornis species complex in Taiwan waters and applied niche modeling to predict its potential range through the end of the 21st Century. The P. damicornis species complex is widespread across shallow, tropical and subtropical waters of the Indo-Pacific regions. Our results revealed that populations from subtropical nonreefal coral communities are P. damicornis, whose native geographical ranges are approximately between 23°N and 35°N. In contrast, those from tropical reefs are P. acuta. Our analysis of 50 environmental data layers demonstrated that the concentrations of CaCO3 polymorphs had the greatest contributions to the distributions of the two species. Future projections under intermediate shared socioeconomic pathways (SSP) 2-4.5 and very high (SSP5-8.5) scenarios of greenhouse gas emissions showed that while sea surface temperature (SST) isotherms would shift northwards, saturation isolines of two CaCO3 polymorphs, calcite (Ωcal) and aragonite (Ωarag), would shift southwards by 2100. Subsequent predictions of future suitable habitats under those conditions indicated that distinct delimitation of geographical ranges for the two species would persist, and neither would extend beyond its native geographical zones, indicating that tropical Taiwan waters are the northern limit for P. acuta. In contrast, subtropical waters are the southern limit for P. damicornis. We concluded that the decline in CaCO3 saturation would make high latitudes less inhabitable, which could be one of the boundary elements that limit poleward range expansion driven by rising SSTs and preserve the latitudinal diversity gradient (LDG) on Earth. Consequently, poleward migration of tropical reef corals to cope with warming oceans should be reevaluated.

Leptoria phrygia in Southern Taiwan shuffles and switches symbionts to resist thermal-induced bleaching.

Symbiodiniaceae communities in some corals often shuffle or switch after severe bleaching events, one of the major threats to coral survival in a world with climate change. In this study we reciprocally transplanted five Leptoria phrygia colonies between two sites with significantly different temperature regimes and monitored them for 12 months. Our ITS2 amplicon deep sequencing demonstrated that L. phrygia acclimatized to maintain a strong and stable association with Durusdinium D17, D. trenchii, and D. glynnii, but also remained flexible and formed a short-term association with different Cladocopium. Most interestingly, two colonies shuffled between Durusdinium and Cladocopium without the occurrence of bleaching; one colony even switched its dominant Cladocopium after generic shuffling. Both dominant Cladocopium were originally rare with relative abundances as low as 0.024%. This is the first record of adult corals switching dominant symbiont without bleaching.

Astaxanthin promotes M2 macrophages and attenuates cardiac remodeling after myocardial infarction by suppression inflammation in rats.

BACKGROUND: Cardiac remodeling after acute myocardial infarction (AMI) is an important process. The present study aimed to assess the protective effects of astaxanthin (ASX) on cardiac remodeling after AMI. METHODS: The study was conducted between April and September 2018. To create a rat AMI model, rats were anesthetized, and the left anterior descending coronary artery was ligated. The rats in the ASX group received 10 mg·kg·day ASX by gavage for 28 days. On the 1st day after AMI, but before ASX administration, six rats from each group were sacrificed to evaluate changes in the heart function and peripheral blood (PB) levels of inflammatory factors. On the 7th day after AMI, eight rats from each group were sacrificed to evaluate the PB levels of inflammatory factors and the M2 macrophage count using both immunofluorescence (IF) and flow cytometry (FC). The remaining rats were observed for 28 days. Cardiac function was examined using echocardiography. The inflammatory factors, namely, tumor necrosis factor-α (TNF-α), interleukin-1ß (IL-1ß), and IL-10, were assessed using enzyme-linked immunosorbent assay. The heart weight/body weight (BW), and lung weight (LW)/BW ratios were calculated, and myocardial fibrosis in the form of collagen volume fraction was measured using Masson trichrome staining. Hematoxylin and eosin (H&E) staining was used to determine the myocardial infarct size (MIS), and TdT-mediated dUTP nick-end labeling staining was used to analyze the myocardial apoptosis index. The levels of apoptosis-related protein, type I/III collagen, transforming growth factor ß1 (TGF-ß1), metalloproteinase 9 (MMP9), and caspase 3 were assessed by Western blotting. Unpaired t-test, one-way analysis of variance, and non-parametric Mann-Whitney test were used to analyze the data. RESULTS: On day 1, cardiac function was worse in the ASX group than in the sham group (left ventricular end-systolic diameter [LVIDs]: 0.72 ±â€Š0.08 vs. 0.22 ±â€Š0.06 cm, t = -11.38; left ventricular end-diastolic diameter [LVIDd]: 0.89 ±â€Š0.09 vs. 0.48 ±â€Š0.05 cm, t = -9.42; end-systolic volume [ESV]: 0.80 [0.62, 0.94] vs. 0.04 [0.03, 0.05] mL, Z = -2.89; end-diastolic volume [EDV]: 1.39 [1.03, 1.49] vs. 0.28 [0.22, 0.32] mL, Z = -2.88; ejection fraction [EF]: 0.40 ±â€Š0.04 vs. 0.86 ±â€Š0.05, t = 10.00; left ventricular fractional shortening [FS] rate: 0.19 [0.18, 0.20] %FS vs. 0.51 [0.44, 0.58] %FS, Z = -2.88, all P < 0.01; n = 6). The levels of inflammatory factors significantly increased (TNF-α: 197.60 [133.89, 237.94] vs. 50.48 [47.21 57.10] pg/mL, Z = -2.88; IL-1ß: 175.23 [160.74, 215.09] vs. 17.78 [16.83, 19.56] pg/mL, Z = -2.88; IL-10: 67.64 [58.90, 71.46] vs. 12.33 [11.64, 13.98] pg/mL, Z = -2.88, all P < 0.01; n = 6). On day 7, the levels of TNF-α and IL-1ß were markedly lower in the ASX group than in the AMI group (TNF-α: 71.70 [68.60, 76.00] vs. 118.07 [106.92, 169.08] pg/mL, F = 42.64; IL-1ß: 59.90 [50.83, 73.78] vs. 151.60 [108.4, 198.36] pg/mL, F = 44.35, all P < 0.01, n = 8). Conversely, IL-10 levels significantly increased (141.84 [118.98, 158.36] vs. 52.96 [42.68, 74.52] pg/mL, F = 126.67, P < 0.01, n = 8). The M2 macrophage count significantly increased (2891.42 ±â€Š211.29 vs. 1583.38 ±â€Š162.22, F = 274.35, P < 0.01 by immunofluorescence test; 0.96 ±â€Š0.18 vs. 0.36 ±â€Š0.05, F = 46.24, P < 0.05 by flowcytometry test). On day 28, cardiac function was better in the ASX group than in the AMI group (LVIDs: 0.50 [0.41, 0.56] vs. 0.64 [0.56, 0.74] cm, Z = -3.60; LVIDd: 0.70 [0.60, 0.76] vs. 0.80 [0.74 0.88] cm, Z = -2.96; ESV: 0.24 [0.18, 0.45] vs. 0.58 [0.44, 0.89] mL, Z = -3.62; EDV: 0.76 [0.44, 1.04] vs. 1.25 [0.82, 1.46] mL, Z = -2.54; EF: 0.60 ±â€Š0.08 vs. 0.50 ±â€Š0.12, F = 160.48; %FS: 0.29 [0.24, 0.31] vs. 0.20 [0.17, 0.21], Z = -4.43, all P < 0.01; n = 16). The MIS and LW/BW ratio were markedly lower in the ASX group than in the AMI group (myocardial infarct size: 32.50 ±â€Š1.37 vs. 50.90 ±â€Š1.73, t = 23.63, P < 0.01, n = 8; LW/BW: 1.81 ±â€Š0.15 vs. 2.17 ±â€Š0.37, t = 3.66, P = 0.01, n = 16). The CVF was significantly lower in the ASX group than in the AMI group: 12.88 ±â€Š2.53 vs. 28.92 ±â€Š3.31, t = 10.89, P < 0.01, n = 8. The expression of caspase 3, TGF-ß1, MMP9, and type I/III collagen was lower in the ASX group than in the AMI group (caspase 3: 0.38 ±â€Š0.06 vs. 0.66 ±â€Š0.04, t = 8.28; TGF-ß1: 0.37 ±â€Š0.04 vs. 0.62 ±â€Š0.07, t = 6.39; MMP9: 0.20 ±â€Š0.06 vs. 0.40 ±â€Š0.06, t = 4.62; type I collagen: 0.42 ±â€Š0.09 vs. 0.74 ±â€Š0.07, t = 5.73; type III collagen: 0.13 ±â€Š0.02 vs. 0.74 ±â€Š0.07, t = 4.32, all P < 0.01; n = 4). CONCLUSIONS: ASX treatment after AMI may promote M2 macrophages and effectively attenuate cardiac remodeling by inhibiting inflammation and reducing myocardial fibrosis.

Demographic census confirms a stable population of the critically-endangered caryophyllid coral Polycyathus chaishanensis (Scleractinia; Caryophyllidae) in the Datan Algal Reef, Taiwan.

Polycyathus chaishanensis is a symbiotic caryophyllid coral described from a single population in a tidal pool off Chaishan, Kaohsiung, Taiwan. Due to its rarity, P. chaishanensis was declared a critically-endangered species under the Taiwan Wildlife Protection Act. In May 2017, a P. chaishanensis colony was discovered in the intertidal area of the Datan Algal Reef, Taoyuan, Taiwan. To determine whether this is a stable population in the algal reef, a demographic census-including data on occurrence, distribution, and colony size-was carried out in the algal reef in southern Taoyuan. Intertidal censuses and sediment collections were conducted at five different sections-Baiyu, Datan G1, Datan G2, Yongxing, and Yongan algal reefs-during the monthly spring low tide from July 2018 to January 2019. In total, 84 colonies-23 in Datan G1 and 61 in Datan G2-were recorded from a tidal range of - 160 to - 250 cm, according to the Taiwan Vertical Datum 2001 compiled by the Central Weather Bureau. No P. chaishanensis was found in Baiyu, Yongxing, or Yongan. The P. chaishanensis colony sizes ranged from 2.55 to 81.5 cm in diameter, with the larger P. chaishanensis present in the lower intertidal zone. Sediment was extremely high, with monthly site averages ranging from 3,818.26 to 29,166.88 mg cm-2 day-1, and there was a significant difference between sites and months, both of which affected the distribution of P. chaishanensis in the algal reef. Our study confirms the existence of a second population of P. chaishanensis in Taiwan, highlighting the importance of the Datan Algal Reef for the survival and protection of this critically-endangered caryophyllid coral and why it is so urgent that the reef should be conserved.

[Promoting the accuracy of chemotherapy medication administration for nurses: an application of root cause analysis].

Drug administration error in the hospital ward is an ever-present problem and an all-too-frequent occurrence. Such errors are often made by nurses who fail to follow relevant nursing standards. The aim of this article was to describe an adverse event of chemotherapy-related medication error that happened in an academic hospital located in central Taiwan. The authors and their colleagues used root cause analysis to survey the adverse event and to suggest ways to improve the accuracy of nurse chemotherapy medication administration. We investigated medication administration of chemotherapy made by nurses between February 24th and 26th, 2008, and found that a number of nurses failed to administer medication properly. Based on data analysis, root causes were identified as: (1) directed prescriptions were unclear, (2) chemotherapy medication administration lacked protocol guidance, (3) education was insufficient and (4) computer systems were inadequately designed. Based on a literature review and matrix analysis, the task force identified four major categories in which improvements were needed. These included: (1) prescription promotion, (2) protocol development and standardization, (3) education for healthcare practitioners and (4) improvement of computer systems. After improvements were put into practices, the accuracy of chemotherapy medication administration by nurses increased to 100%. We shared the promotion experience with clinical managers to analyze and avoid adverse events.

Temporal variation and photochemical efficiency of species in Symbiodinaceae associated with coral Leptoria phrygia (Scleractinia; Merulinidae) exposed to contrasting temperature regimes.

The Symbiodinaceae are paradoxical in that they play a fundamental role in the success of scleractinian corals, but also in their dismissal when under stress. In the past decades, the discovery of the endosymbiont's genetic and functional diversity has led people to hope that some coral species can survive bleaching events by associating with a stress-resistant symbiont that can become dominant when seawater temperatures increase. The variety of individual responses encouraged us to scrutinize each species individually to gauge its resilience to future changes. Here, we analyse the temporal variation in the Symbiodinaceae community associated with Leptoria phrygia, a common scleractinian coral from the Indo-Pacific. Coral colonies were sampled from two distant reef sites located in southern Taiwan that differ in temperature regimes, exemplifying a 'variable site' (VS) and a 'steady site' (SS). We investigated changes in the relative abundance of the dominant symbiont and its physiology every 3-4 months from 2016-2017. At VS, 11 of the 12 colonies were dominated by the stress-resistant Durusdinium spp. (>90% dominance) and only one colony exhibited co-dominance between Durusdinium spp. and Cladocopium spp. Every colony displayed high photochemical efficiency across all sampling periods, while showing temporal differences in symbiont density and chlorophyll a concentration. At SS, seven colonies out of 13 were dominated by Cladocopium spp., five presented co-dominance between Durusdinium spp./Cladocopium spp. and only one was dominated by Durusdinium spp. Colonies showed temporal differences in photochemical efficiency and chlorophyll a concentration during the study period. Our results suggest that VS colonies responded physiologically better to high temperature variability by associating with Durusdinium spp., while in SS there is still inter-colonial variability, a feature that might be advantageous for coping with different environmental changes.

[Strategies for discussing death with child cancer sufferers].

Since a curriculum concerning life and death was established and palliative care began to be promoted, people have gradually awakened to the needs of dying patients. Because of the nature of oriental culture, however, ultimate decisions concerning someone with a terminal disease have traditionally been made by family, so dying patients, especially children with cancer, have usually not been told of their true condition. The purpose of this article was to gain an understanding of the necessity of talking about death with child cancer patients and how to communicate with these children. The results show that helping the family to talk about death and decision making concerning treatment can help them to adapt to the grieving period when the children pass away. The tactics that nurses can use for communication with dying children include: to acknowledge the decision maker in the family, adopt the concept of death appropriate to a person of the child's age, discuss the prognosis for the development of the disease, and opt to use the medium of communication. The findings of this article may serve as a source of reference for nurses caring for dying children, and cause greater attention to be paid to these issues.

Correction: Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae.

[This corrects the article DOI: 10.1371/journal.pone.0179055.].

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae.

Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.

[Nipple confusion and breastfeeding: a literature review].

Among the ten steps to successful breastfeeding advocated by the WHO and UNICEF, steps six and nine clearly state that formula supplementation and pacifier use, except when medically necessary, should be avoided. Early formula supplementation may not only interfere with the mother's lactation but also result in nipple confusion on the part of the baby. To avoid nipple confusion, the encouragement of cup feeding and the non-provision of pacifiers or bottles are required nursing practice in baby-friendly hospitals. However, the relationship between nipple confusion and the duration of breastfeeding has not been well examined. The purpose of this paper is to explore the relationships between three methods of feeding (i.e. pacifier, bottle feeding, and cup feeding), nipple confusion, and duration of breastfeeding. A hypothetical framework is proposed to explain these relationships on the basis of a review of the literature.

[Effect of very early kangaroo care on extrauterine temperature adaptation in newborn infants with hypothermia problems].

Increased morbidity and mortality has been associated with neonates admitted with body temperatures below 36 degrees C. We employed an experimental design in a randomized control trial to compare the effectiveness of using early kangaroo care (KC) for extrauterine temperature adaptation against that of using radiant warmers. Trial subjects included 78 consecutive cesarean newborn infants with hypothermia problems. The KC group received skin-to-skin contact with their mothers in the post-operative room, while infants in the control group received routine care under radiant warmers. The mean temperature of the KC group was slightly higher than that of the control group (36.29 degrees C vs. 36.22 degrees C, p = .044). After four hours, 97.43% of KC group infants had reached normal body temperatures, compared with 82.05% in the radiant warmer group. Results demonstrate the positive effects of KC for extrauterine temperature adaptation in hypothermia infants. In the course of evidence-based practice, KC could be incorporated into the standard care regimen in order to improve hypothermia care.

Winding paths to simplicity: genome evolution in facultative insect symbionts.

Symbiosis between organisms is an important driving force in evolution. Among the diverse relationships described, extensive progress has been made in insect­bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. Particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. To bridge the gap between those obligate symbionts with extremely reduced genomes and their non-host-restricted ancestors, this review focuses on the recent progress in genome characterization of facultative insect symbionts. Notable cases representing various types and stages of host associations, including those from multiple genera in the family Enterobacteriaceae (class Gammaproteobacteria), Wolbachia (Alphaproteobacteria) and Spiroplasma (Mollicutes), are discussed. Although several general patterns of genome reduction associated with the adoption of symbiotic relationships could be identified, extensive variation was found among these facultative symbionts. These findings are incorporated into the established conceptual frameworks to develop a more detailed evolutionary model for the discussion of possible trajectories. In summary, transitions from facultative to obligate symbiosis do not appear to be a universal one-way street; switches between hosts and lifestyles (e.g. commensalism, parasitism or mutualism) occur frequently and could be facilitated by horizontal gene transfer.

Thioredoxin-Interacting Protein Mediates NLRP3 Inflammasome Activation Involved in the Susceptibility to Ischemic Acute Kidney Injury in Diabetes.

Kidney in diabetic state is more sensitive to ischemic acute kidney injury (AKI). However, the underlying mechanisms remain unclear. Herein, we examined the impact of diabetes mellitus on thioredoxin-interacting protein (TXNIP) expression and whether mediated NLRP3 activation was associated with renal ischemia/reperfusion- (I/R-) induced AKI. In an in vivo model, streptozotocin-induced diabetic rats showed higher susceptibility to I/R injury with increased TXNIP expression, which was significantly attenuated by resveratrol (RES) treatment (10 mg/kg intraperitoneal daily injection for 7 consecutive days prior to I/R induction). RES treatment significantly inhibited TXNIP binding to NLRP3 in diabetic rats subjected to renal I/R injury. Furthermore, RES treatment significantly reduced cleaved caspase-1 expression and production of IL-1ß and IL-18. In an in vitro study using cultured human kidney proximal tubular cell (HK-2 cells) in high glucose condition (HG, 30 mM) subjected to hypoxia/reoxygenation (H/R), HG combined H/R (HH/R) stimulated TXNIP expression which was accompanied by increased NLRP3 expression, ROS generation, caspase-1 activity and IL-1ß levels, and aggravated HK-2 cells apoptosis. All these changes were significantly attenuated by TXNIP RNAi and RES treatment. In conclusion, our results demonstrate that TXNIP-mediated NLRP3 activation through oxidative stress is a key signaling mechanism in the susceptibility to AKI in diabetic models.

Complete Genome Sequence of Agrobacterium tumefaciens Ach5.

Agrobacterium tumefaciens is a phytopathogenic bacterium that causes crown gall disease. The strain Ach5 was isolated from yarrow (Achillea ptarmica L.) and is the wild-type progenitor of other derived strains widely used for plant transformation. Here, we report the complete genome sequence of this bacterium.

De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation.

Coconut palm (Cocos nucifera) is a symbol of the tropics and a source of numerous edible and nonedible products of economic value. Despite its nutritional and industrial significance, coconut remains under-represented in public repositories for genomic and transcriptomic data. We report de novo transcript assembly from RNA-seq data and analysis of gene expression in seed tissues (embryo and endosperm) and leaves of a dwarf coconut variety. Assembly of 10 GB sequencing data for each tissue resulted in 58,211 total unigenes in embryo, 61,152 in endosperm, and 33,446 in leaf. Within each unigene pool, 24,857 could be annotated in embryo, 29,731 could be annotated in endosperm, and 26,064 could be annotated in leaf. A KEGG analysis identified 138, 138, and 139 pathways, respectively, in transcriptomes of embryo, endosperm, and leaf tissues. Given the extraordinarily large size of coconut seeds and the importance of small RNA-mediated epigenetic regulation during seed development in model plants, we used homology searches to identify putative homologs of factors required for RNA-directed DNA methylation in coconut. The findings suggest that RNA-directed DNA methylation is important during coconut seed development, particularly in maturing endosperm. This dataset will expand the genomics resources available for coconut and provide a foundation for more detailed analyses that may assist molecular breeding strategies aimed at improving this major tropical crop.

Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads.

Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo-cycad sister-group hypothesis.

Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera).

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.

The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction.

We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IR(A)). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants.