Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.

The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome. Little is known about the recent evolution of the Y chromosome because only the human Y chromosome has been fully sequenced. Prevailing theories hold that Y chromosomes evolve by gene loss, the pace of which slows over time, eventually leading to a paucity of genes, and stasis. These theories have been buttressed by partial sequence data from newly emergent plant and animal Y chromosomes, but they have not been tested in older, highly evolved Y chromosomes such as that of humans. Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, achieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor. We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, 'genetic hitchhiking' effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour. Although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.

Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers.

Ovarian carcinomas with mutations in the tumour suppressor BRCA2 are particularly sensitive to platinum compounds. However, such carcinomas ultimately develop cisplatin resistance. The mechanism of that resistance is largely unknown. Here we show that acquired resistance to cisplatin can be mediated by secondary intragenic mutations in BRCA2 that restore the wild-type BRCA2 reading frame. First, in a cisplatin-resistant BRCA2-mutated breast-cancer cell line, HCC1428, a secondary genetic change in BRCA2 rescued BRCA2 function. Second, cisplatin selection of a BRCA2-mutated pancreatic cancer cell line, Capan-1 (refs 3, 4), led to five different secondary mutations that restored the wild-type BRCA2 reading frame. All clones with secondary mutations were resistant both to cisplatin and to a poly(ADP-ribose) polymerase (PARP) inhibitor (AG14361). Finally, we evaluated recurrent cancers from patients whose primary BRCA2-mutated ovarian carcinomas were treated with cisplatin. The recurrent tumour that acquired cisplatin resistance had undergone reversion of its BRCA2 mutation. Our results suggest that secondary mutations that restore the wild-type BRCA2 reading frame may be a major clinical mediator of acquired resistance to platinum-based chemotherapy.

Fungal endophytes of the obligate parasitic dwarf mistletoe Arceuthobium americanum (Santalaceae) act antagonistically in vitro against the native fungal pathogen Cladosporium (Davidiellaceae) of their host.

PREMISE OF THE STUDY: Endophytic fungi likely occur in all plants, yet little is known about those of parasitic plants, despite their potential to influence parasite success. Arceuthobium americanum is a parasitic angiosperm that greatly compromises the North American timber industry. We hypothesized that (1) A. americanum hosts fungal endophytes, and (2) these endophytes help A. americanum resist infection by fungal pathogens. • METHODS: Healthy A. americanum stem and fruit tissues were differentially stained for cellulose and chitin and visualized using fluorescence microscopy. Stem sections (sterilized vs. unsterilized) and seeds were incubated on agar plates to cultivate fungi, both to extract DNA for ITS rDNA sequencing and to observe interactions with native fungi from unsterilized specimens. • KEY RESULTS: Aside from xylem vessel elements, fungal structures were observed in all tissues, including those of the embryo. The ITS sequences of fungi cultured from internal tissues closely matched those of the known endophytes Phoma, Sydowia, and Phacidiopycnis, while those of surface organisms closely matched Cladosporium spp. Cultured fungi from internal tissues (putative endophytes) inhibited the growth of the surface organisms without affecting the other endophytes. • CONCLUSION: Fungal communities are established in A. americanum stems as well as in fruits and seeds, suggesting vertical transmission. These internally derived fungi act antagonistically toward fungi with pathogenic tendencies. As such, native mistletoe endophytes might protect A. americanum against fungal pathogens in nature. In the future, manipulation of endophytes might be a component of mistletoe control programs.

Analysis of the DNA sequence and duplication history of human chromosome 15.

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.

Bioactivity and the first transmission electron microscopy immunogold studies of short de novo-designed antimicrobial peptides.

In light of the era of microbial drug resistance, the current study aimed to better understand the relationships between sequence, higher-order structure, and mechanism of action for five designed peptides against multidrug-resistant (MDR) pathogens. All peptides studied were 15 residues long, were polycationic, adopted alpha-helical structures within hydrophobic environments (excluding the d-amino acid-substituted peptide MA-d), and contained N-terminal glycine residues, a novel antimicrobial peptide (AMP) design principle. Increasing hydrophobicity enhanced MICs (≤500 µg/ml to ≤7.4 µg/ml) without significantly increasing hemolytic activity (18% maximum hemolysis at 3,400 µg/ml). To the best of our knowledge, this is the first study to have successfully adapted and used a transmission electron microscopy (TEM) immunogold method to investigate the mechanism of action of short (∼15 residues long) AMPs within bacteria. We propose a "floodgate" mechanism to possibly explain membrane deformation and the relative absence of membrane-associated peptides 10 h into incubation.

Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication.

Human subtelomeres are polymorphic patchworks of interchromosomal segmental duplications at the ends of chromosomes. Here we provide evidence that these patchworks arose recently through repeated translocations between chromosome ends. We assess the relative contribution of the principal mechanisms of ectopic DNA repair to the formation of subtelomeric duplications and find that non-homologous end-joining predominates. Once subtelomeric duplications arise, they are prone to homology-based sequence transfers as shown by the incongruent phylogenetic relationships of neighbouring sections. Interchromosomal recombination of subtelomeres is a potent force for recent change. Cytogenetic and sequence analyses reveal that pieces of the subtelomeric patchwork have changed location and copy number with unprecedented frequency during primate evolution. Half of the known subtelomeric sequence has formed recently, through human-specific sequence transfers and duplications. Subtelomeric dynamics result in a gene duplication rate significantly higher than the genome average and could have both advantageous and pathological consequences in human biology. More generally, our analyses suggest an evolutionary cycle between segmental polymorphisms and genome rearrangements.

Human subtelomeric WASH genes encode a new subclass of the WASP family.

Subtelomeres are duplication-rich, structurally variable regions of the human genome situated just proximal of telomeres. We report here that the most terminally located human subtelomeric genes encode a previously unrecognized third subclass of the Wiskott-Aldrich Syndrome Protein family, whose known members reorganize the actin cytoskeleton in response to extracellular stimuli. This new subclass, which we call WASH, is evolutionarily conserved in species as diverged as Entamoeba. We demonstrate that WASH is essential in Drosophila. WASH is widely expressed in human tissues, and human WASH protein colocalizes with actin in filopodia and lamellipodia. The VCA domain of human WASH promotes actin polymerization by the Arp2/3 complex in vitro. WASH duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires vary. Thus, human subtelomeres are not genetic junkyards, and WASH's location in these dynamic regions could have advantageous as well as pathologic consequences.

Elevated rates of sister chromatid exchange at chromosome ends.

Chromosome ends are known hotspots of meiotic recombination and double-strand breaks. We monitored mitotic sister chromatid exchange (SCE) in telomeres and subtelomeres and found that 17% of all SCE occurs in the terminal 0.1% of the chromosome. Telomeres and subtelomeres are significantly enriched for SCEs, exhibiting rates of SCE per basepair that are at least 1,600 and 160 times greater, respectively, than elsewhere in the genome.

Early reproductive developmental anatomy in Decaisnea (Lardizabalaceae) and its systematic implications.

BACKGROUND AND AIMS: Decaisnea insignis, known as 'dead man's fingers' (Lardizabalaceae), is widely distributed in China and the Himalayan foothill countries. This economically important plant, which is the only species in the genus, has not been the subject of any embryological studies aside from one brief, older paper that lacks micrographs. Data on Decaisnea are also important because its systematic position has been unstable since the genus was established in 1855. Therefore, the objectives of this study were: (a) to use modern microscopy to document early reproductive anatomical development in Decaisnea; and (b) to compare qualitatively these early embryological characters with allied taxa in a systematic context. METHODS: Decaisnea insignis floral buds and inflorescences were regularly collected from Shaanxi Province, China and prepared for light microscopy. The embryological characters studied were qualitatively compared with those of allied taxa via a thorough examination of the existing literature. KEY RESULTS: Early reproductive anatomy in Decaisnea was documented and novel revelations made. It was discovered that the pollen is shed when three-celled (not two-celled, as previously reported), and that endosperm formation is nuclear (not cellular or helobial, as previously reported). These two newly revealed embryological characters are not found in any other members of Lardizabalaceae. Furthermore, neither are persistent antipodal cells, which we confirmed to be present in Decaisnea. CONCLUSIONS: Decaisnea and other Lardizabalaceae characteristically have tetrasporangiate anthers, a secretory tapetum, simultaneous microsporocyte cytokinesis, primarily bitegmic, crassinucellate ovules, and a Polygonum type embryo sac. However, in the family, persistent antipodals, nuclear endosperm, and pollen shed at the three-celled stage are only found in Decaisnea. These embryological data prompted the suggestion that Decaisnea needs elevation above the level of genus.

Adaptive phenotypic plasticity of Pseudoroegneria spicata: response of stomatal density, leaf area and biomass to changes in water supply and increased temperature.

BACKGROUND AND AIMS: Changes in rainfall and temperature brought about through climate change may affect plant species distribution and community composition of grasslands. The primary objective of this study was to test how manipulation of water and temperature would influence the plasticity of stomatal density and leaf area of bluebunch wheatgrass, Pseudoroegneria spicata. It was hypothesized that: (1) an increased water supply will increase biomass and leaf area and decrease stomatal density, while a reduced water supply will cause the opposite effect; (2) an increase in temperature will reduce biomass and leaf area and increase stomatal density; and (3) the combinations of water and temperature treatments can be aligned along a stress gradient and that stomatal density will be highest at high stress. Methods The three water supply treatments were (1) ambient, (2) increased approx. 30% more than ambient through weekly watering and (3) decreased approx. 30 % less than ambient by rain shades. The two temperature treatments were (1) ambient and (2) increased approx. 1-3 degrees C by using open-top chambers. At the end of the second experimental growing season, above-ground biomass was harvested, oven-dried and weighed, tillers from bluebunch wheatgrass plants sampled, and the abaxial stomatal density and leaf area of tillers were measured. KEY RESULTS: The first hypothesis was partially supported--reducing water supply increased stomatal density, but increasing water supply reduced leaf area. The second hypothesis was rejected. Finally, the third hypothesis could not be fully supported--rather than a linear response there appears to be a parabolic stomatal density response to stress. CONCLUSIONS: Overall, the abaxial stomatal density and leaf area of bluebunch wheatgrass were plastic in their response to water and temperature manipulations. Although bluebunch wheatgrass has the potential to adapt to changing climate, the grass is limited in its ability to respond to a combination of reduced water and increased temperature.

Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers.

BACKGROUND: Mallotus oblongifolius, an evergreen shrub endemic to Hainan Island, China, is important both medicinally and economically. Due to its special medicinal significance and the continuing rise of market demand, its populations in the wild have been subject to long-term illegal and unrestrained collection. Hence, an evaluation of genetic variability is essential for the conservation and genetic reserve development of this species. METHODS: Sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and genetic structure of 20 natural populations of M. oblongifolius growing in different eco-geographical regions of Hainan Island, China. RESULTS: We revealed a considerable genetic diversity (h = 0.336, I = 0.5057, SRAP markers; h = 0.3068, I = 0.4657, ISSR markers) and weak genetic differentiation (Gst = 0.2764 for SRAP, Gst = 0.2709 for ISSR) with the same gene flow (Nm = 1.3092 for SRAP, Nm = 1.346 for ISSR) among the M. oblongifolius populations. The Mantel Test showed that the distribution of genetic variation among populations could not be explained by the pronounced geographical distances (r = 0.01255, p = 0.5538). All results of the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), Neighbor-joining (NJ), Principal Coordinate Analysis (PCoA) and Bayesian analyses supported a habitat-specific genetic clustering model for M. oblongifolius, indicating a local adaptive divergence for the studied populations. DISCUSSION: We suggested that the habitat fragmentation and specificity for M. oblongifolius populations weakened the natural gene flow and promoted an adaptation to special habitats, which was the main reason for local adaptive divergence among M. oblongifolius.

Correction: Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties.

[This corrects the article DOI: 10.1371/journal.pone.0198517.].

Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties.

Anthropogenic processes and socio-economic factors play important roles in shaping plant diversity in urban parks. To investigate how plant diversity of Ma' anling urban volcano park in Hainan Province, China respond to these factors, we carried out a field investigation on the taxonomic and phylogenetic diversity of vascular plants and soil properties in this area. We found 284 species of vascular plants belonging to 88 families and 241 genera, which included 194 native species, 23 invasive species, 31 naturalized species, 40 cultivars, and 4 rare / endangered plant species. Tree composition and richness significantly varied between different vegetation formations (plantation, secondary forest, and abandoned land). Plant species richness and community composition were significantly affected by elevation (El), soil water content (WC), total soil nitrogen (TN) and soil organic matter (SOM). There were significant diversity differences between plantations and abandoned lands, but not between the plantations and secondary forests. The flora in the study site was tropical in nature, characterized by pantropic distributions. Compared to adjacent areas, floristic composition in the study site was most similar to that of Guangdong, followed by that of Vietnam. Our study revealed the diversity patterns of volcanic plants and provided the basis for future planning of plant conservation, such as preserving plant species, maintaining plant habitats, and coordinating plant management in this region.

Author Correction: Thermogenesis-triggered seed dispersal in dwarf mistletoe.

This corrects the article DOI: 10.1038/ncomms7262.

Complete plastome sequence of Dracaena cambodiana (Asparagaceae): a species considered "Vulnerable" in Southeast Asia.

Dracaena cambodiana (Asparagaceae) is a treelike plant ranging from 3 to 10 m tall. It grows in low-elevation forests (0-300 m) having dry and sandy soils. It is distributed in Southern Hainan Island in China and other Southeast Asian countries (e.g. Cambodia, Laos, Thailand and Vietnam). The dried resin can be used medicinally as a substitute for that of Dracaena cochinchinensis. It has been ranked as a Vulnerable (VU) species in China. Here we report and characterize the complete plastid genome sequence of D. cambodiana. The complete plastome is 156,697 bp in length. It contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,526 bp, a Large Single-Copy (LSC) region of 84,988 bp and a Small Single-Copy (SSC) region of 18,657 bp. The plastome contains 113 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, four unique rRNA genes and three pseudogenes (i.e. matK, infA, ndhF). The overall A/T content in the plastome of D. cambodiana is 62.4%. We performed phylogenetic analyses using the entire plastome, including spacers, introns, etc., and we determined that D. cambodiana and Maianthemum bicolor were closely related. The complete plastome sequence of D. cambodiana will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Asparagales.

Variation of Soil Bacterial Communities in a Chronosequence of Rubber Tree (Hevea brasiliensis) Plantations.

Regarding rubber tree plantations, researchers lack a basic understanding of soil microbial communities; specifically, little is known about whether or not soil microbial variation is correlated with succession in these plantations. In this paper, we used high-throughput sequencing of the 16S rRNA gene to investigate the diversity and composition of the soil bacterial communities in a chronosequence of rubber tree plantations that were 5, 10, 13, 18, 25, and 30 years old. We determined that: (1) Soil bacterial diversity and composition show changes over the succession stages of rubber tree plantations. The diversity of soil bacteria were highest in 10, 13, and 18 year-old rubber tree plantations, followed by 30 year-old rubber tree plantations, whereas 5 and 25 year-old rubber tree plantations had the lowest values for diversity. A total of 438,870 16S rDNA sequences were detected in 18 soil samples from six rubber tree plantations, found in 28 phyla, 66 classes, 139 orders, 245 families, 355 genera, and 645 species, with 1.01% sequences from unclassified bacteria. The dominant phyla were Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria, and Verrucomicrobia (relative abundance large than 3%). There were differences in soil bacterial communities among different succession stages of rubber tree plantation. (2) Soil bacteria diversity and composition in the different stages was closely related to pH, vegetation, soil nutrient, and altitude, of which pH, and vegetation were the main drivers.

Use of fluorescent sequence-specific polyamides to discriminate human chromosomes by microscopy and flow cytometry.

In this paper, we demonstrate the use of synthetic polyamide probes to fluorescently label heterochromatic regions on human chromosomes for discrimination in cytogenetic preparations and by flow cytometry. Polyamides bind to the minor groove of DNA in a sequence-specific manner. Unlike conventional sequence-specific DNA or RNA probes, polyamides can recognize their target sequence without the need to subject chromosomes to harsh denaturing conditions. For this study, we designed and synthesized a polyamide to target the TTCCA-motif repeated in the heterochromatic regions of chromosome 9, Y and 1. We demonstrate that the fluorescently labeled polyamide binds to its target sequence in both conventional cytogenetic preparations of metaphase chromosomes and suspended chromosomes without denaturation. Chromosomes 9 and Y can be discriminated and purified by flow sorting on the basis of polyamide binding and Hoechst 33258 staining. We generate chromosome 9- and Y-specific 'paints' from the sorted fractions. We demonstrate the utility of this technology by characterizing the sequence of an olfactory receptor gene that is duplicated on multiple chromosomes. By separating chromosome 9 from chromosomes 10-12 on the basis of polyamide fluorescence, we determine and differentiate the haplotypes of the highly similar copies of this gene on chromosomes 9 and 11.

Identification of Combinatorial Genomic Abnormalities Associated with Prostate Cancer Early Recurrence.

Multiple biomarkers are needed to distinguish aggressive from indolent prostate cancer. We tested the prognostic utility of a three-marker fluorescent in situ hybridization (FISH) panel (TMPRSS2/ERG rearrangements, AR gain, and PTEN deletion) in a retrospective cohort (n = 210; median follow-up, 5.7 years). PTEN deletion was associated with an increased risk of biochemical recurrence (BcR; hazard ratio, 3.58; 95% CI, 1.39-9.22; P < 0.01) by multivariable Cox regression analyses and earlier BcR (P < 0.02) by Kaplan-Meier analysis. AR gain coexisted with X-chromosome gain and was associated with advanced tumor stage. When this panel was applied, two categories of combinatorial abnormalities proved clinically important. First, PTEN deletion without TMPRSS2/ERG rearrangement was enriched in pT3/4 tumors (70% versus 48%) and tumors with Gleason grades of 8 to 9 (60% versus 17%) compared with the entire cohort. These patients had earlier BcR than patients with normal FISH panel results (P < 0.01). In contrast, patients with PTEN deletion and ERG rearrangement had a BcR rate similar to patients who tested normal for all three markers (P > 0.1). Second, AR gain and concurrent trisomy 10 without TMPRSS2/ERG rearrangement were enriched in pT3/4 tumors and tumors with Gleason grades of 8 to 9. The three-marker FISH panel demonstrated prognostic utility and identified genomic aberrations associated with advanced disease state and early BcR in prostate cancer.

Thermogenesis-triggered seed dispersal in dwarf mistletoe.

Lodgepole pine dwarf mistletoe (DM), Arceuthobium americanum, is a parasitic flowering plant and forest pathogen in North America. Seed dispersal in DM occurs by explosive discharge. Notably, slight warming of ripe DM fruit in the laboratory can trigger explosions. Previously, we showed that alternative oxidase, a protein involved in endogenous heat production (thermogenesis) in plants, is present in DM fruit. These observations have led us to investigate if thermogenesis induces discharge. Here, infrared thermographs reveal that ripe DM fruits display an anomalous increase in surface temperature by an average of 2.1±0.8 °C over an average time of 103±29 s (n=9, 95% confidence interval) before dehiscence. Furthermore, both non-isothermal and isothermal modulated differential scanning calorimetry consistently show an exothermic event (~1 J g(-1)) in the non-reversible heat flow just prior to discharge. These results support thermogenesis-triggered seed discharge, never before observed in any plant.