Flow cytometry reveals that the rust fungus,Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported—2489 Mbp

Among the Eukaryotes, Fungi have relatively small genomes (average of 44.2 Mbp across 1850 species). The order Pucciniales (Basidiomycota) has the largest average genome size among fungi (305 Mbp), and includes the two largest fungal genomes reported so far (Puccinia chrysanthemi and Gymnosporangium confusum, with 806.5 and 893.2 Mbp, respectively). In this work, flow cytometry was employed to determine the genome size of the Bidens pilosa rust pathogen, Uromyces bidentis. The results obtained revealed that U. bidentis presents a surprisingly large haploid genome size of 2489 Mbp. This value is almost three times larger than the previous largest fungal genome reported and over 50 times larger than the average fungal genome size. Microscopic examination of U. bidentis nuclei also showed that they are not as different in size from the B. pilosa nuclei when compared with the differences between other rusts and their host plants. This result further reinforces the position of the Pucciniales as the fungal group with the largest genomes, prompting studies addressing the role of repetitive elements and polyploidy in the evolution, pathological specialization and diversity of fungal species.     

The rhomboids: a near ubiquitous family of intramembrane serine proteases evolved via multiple horizontal gene transfers

Background  

The rhomboid family consists of polytopic membrane proteins, which show a level of evolutionary conservation that is unique among membrane proteins. The rhomboids are present in nearly all sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. On the basis of experimental studies with the developmental regulator Rhomboid from Drosophila and the AarA protein from the bacterium Providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose signaling function is conserved in eukaryotes and prokaryotes.     

Egg environments have large effects on embryonic development,but have minimal consequences for hatchling phenotypes in an invasive lizard

Plastic responses of embryos to developmental environments can shape phenotypes in ways that impact fitness. The mechanisms by which developmental conditions affect offspring phenotypes vary substantially among taxa and are poorly understood in most systems. In this study, we evaluate the effects of thermal and hydric conditions on patterns of egg water uptake, embryonic development and yolk metabolism in embryos of the lizard Anolis sagrei to gain insights into how these factors shape morphological variation in hatchlings. Our 3 × 2 experimental design (3 thermal and 2 hydric conditions) revealed that developmental temperature has strong effects on rates of development and yolk metabolism, but the impacts of moisture were minimal. Increased water uptake by eggs under relatively wet conditions resulted in larger hatchlings with less internalized residual yolk than hatchlings from dry‐incubated eggs. However, the relatively small phenotypic differences among treatments may have small fitness consequences. These results demonstrate that embryos of A. sagrei can tolerate a broad range of environmental conditions without substantial impacts on critical morphological traits. Such embryonic tolerances may facilitate colonization and establishment in novel environments. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 25–41.     

Life history consequences of feeding versus non-feeding in a facultatively non-feeding toad larva

Summary Bufo periglenes, a toad endemic to montane Costa Rica, produces an unusually small clutch of large, yolk-rich eggs. The toads breed in small ephemeral pools that are unpredictable in duration and may be low in food availability. Two congeners, Bufo coniferus and Bufo marinus, occur nearby, breed in more permanent bodies of water that offer more food, and exhibit the typical toad pattern of large clutches of small eggs. Tadpoles of all three species feed on detritus and suspended organic material. By raising tadpoles of the three species individually with and without food I investigated the relationship between egg size (yolk provision) and tadpole survival. All of the unfed B. coniferus and B. marinus tadpoles grew little and died soon after developing to the hindlimb bud stage. On the other hand, all of the unfed B. periglenes tadpoles metamorphosed successfully, demonstrating that the tadpoles are facultatively non-feeding; developmental time from hatching to metamorphosis was significantly shorter for unfed tadpoles than for fed tadpoles, but fed individuals were significantly larger at transformation. Faster developmental rate and larger body size at transformation are both advantageous for frogs and toads, but cannot be attained simultaneously. Large egg size may afford flexibility in unpredictable environments. In pools where food is available, tadpoles presumably eat, take longer to metamorphose, but are larger at transformation than tadpoles developing in nutrient-poor sites. Small body size at transformation (a consequence of not eating) has potential costs, but the large quantity of yolk provided by a large egg enhances the probability of metamorphosis in food-limited environments.     

GENOMIC COADAPTATION AND DEVELOPMENTAL STABILITY WITHIN INTROGRESSED POPULATIONS OF ENNEACANTHUS GLORIOSUS AND E. OBESUS (PISCES,CENTRARCHIDAE)

Using fluctuating bilateral asymmetry as a measure of developmental stability, we tested the hypothesis that genomic coadaptation mediates developmental stability in natural populations. Hybrid populations were more asymmetrical than populations of the parental species, and ranks of overall developmental instability were positively correlated with ranks of mean heterozygosity in these populations. The failure to find increased asymmetry in previous studies of natural hybrid populations (Jackson, 1973a, 1973b; Felley, 1980) suggests that such populations may have re-evolved coadapted genomes. Increased asymmetry in hybrid Enneacanthus populations may reflect the youthfulness of these populations.     

Genetic drift and mutational hazard in the evolution of salamander genomic gigantism

Salamanders have the largest nuclear genomes among tetrapods and, excepting lungfishes, among vertebrates as a whole. Lynch and Conery (2003) have proposed the mutational‐hazard hypothesis to explain variation in genome size and complexity. Under this hypothesis, noncoding DNA imposes a selective cost by increasing the target for degenerative mutations (i.e., the mutational hazard). Expansion of noncoding DNA, and thus genome size, is driven by increased levels of genetic drift and/or decreased mutation rates; the former determines the efficiency with which purifying selection can remove excess DNA, whereas the latter determines the level of mutational hazard. Here, we test the hypothesis that salamanders have experienced stronger long‐term, persistent genetic drift than frogs, a related clade with more typically sized vertebrate genomes. To test this hypothesis, we compared dN/dS and Kr/Kc values of protein‐coding genes between these clades. Our results do not support this hypothesis; we find that salamanders have not experienced stronger genetic drift than frogs. Additionally, we find evidence consistent with a lower nucleotide substitution rate in salamanders. This result, along with previous work showing lower rates of small deletion and ectopic recombination in salamanders, suggests that a lower mutational hazard may contribute to genomic gigantism in this clade.     

Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea <Emphasis Type="Italic">Calyptogena</Emphasis> clams

To understand reductive genome evolution (RGE), we comparatively analyzed the recently reported small genomes of two chemoautotrophic, intracellular symbionts of deep-sea clams, Calyptogena okutanii and C. magnifica. Both genomes lack most genes for DNA recombination and repair such as recA and mutY. Their genome architectures were highly conserved except one inversion. Many deletions from small (<100 bp) to large (1–11 kbp) sizes were detected and the deletion numbers decreased exponentially with size. Densities of deletions and short-repeats, as well as A+T content were higher in non-coding regions than in coding regions. Because Calyptogena symbiont genomes lack recA, we propose that deletions and the single inversion occurred by RecA-independent recombination (RIR) at short-repeats with simultaneous consumption of repeats, and that short-repeats were regenerated by accelerated mutations with enhanced A+T bias due to the absence of mutY. We further propose that extant Calyptogena symbiont genomes are in an actively reducing stage of RGE consisting of small and large deletions, and the deletions are caused by short-repeat dependent RIR along with regeneration of short-repeats. In future, the RGE rate will slowdown when the gene repertoires approach the minimum gene set necessary for intracellular symbiotic life. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. H. Kuwahara and Y. Takaki equally contributed to this work.     

PULSED‐FIELD GEL ELECTROPHORESIS ANALYSIS OF GENOME SIZE AND STRUCTURE IN PAVLOVA GYRANS AND DIACRONEMA SP. (HAPTOPHYTA)1

Information regarding genome size and structure is a prerequisite for selecting model organisms and for facilitating the most efficient study of their chromosomal DNA. The goal of this study was to identify future candidates for complete‐genome‐sequencing projects among economically or evolutionarily important species of haptophyte algae. Using pulsed‐field gel electrophoresis (PFGE), we identified relatively small genomes and chromosome sizes in two haptophyte species from the class Pavlovophyceae, Pavlova gyrans Butcher and Diacronema sp. The basal position of Pavlovophyceae in the Haptophyta; the key position of this group in the chromalveolates; and their economic and potential biomedical importance, ease of culturing, and small genome size make these taxa ideal models for complete‐genome sequencing.     

头花杜鹃、陇蜀杜鹃及杜鹃属植物叶绿体基因组比较分析

头花杜鹃(Rhododendron capitatum)和陇蜀杜鹃(R. przewalskii)是极具观赏价值的野生花卉和药用植物。为探讨头花杜鹃和陇蜀杜鹃叶绿体基因组的遗传结构及进化特征,该研究利用 Illumina HiSeq 4000 平台对头花杜鹃和陇蜀杜鹃的叶绿体全基因组进行测序,经组装和注释后,结合 7 个已发表的杜鹃属植物叶绿体全基因组进行比较基因组学分析和系统发育分析。结果表明:(1)头花杜鹃和陇蜀杜鹃叶绿体全基因组呈典型的环状四分体结构,均由一个大单拷贝区(105 990、109 191 bp)、一个小单拷贝区(2 617、2 606 bp)和一对反向重复区(45 825、47 516 bp)构成,全长分别为200 257、206 829 bp。(2)头花杜鹃和陇蜀杜鹃叶绿体基因组中共鉴定出 263 个SSR位点,大部分 SSR 偏好使用 A/T 碱基,密码子偏好使用 A/U 结尾。(3)杜鹃属植物叶绿体全基因组中普遍存在基因丢失以及基因组重排等结构变异现象。该研究丰富了杜鹃属植物的基因组资源,为头花杜鹃、陇蜀杜鹃的资源开发、遗传进化、育种及系统发育相关研究提供了理论参考。     

Plastic responses of some life history traits and cellular components of body size in Aphidius ervi as related to the age of its host Acyrthosiphon pisum

Phenotypic plasticity of wing size and shape has been evaluated in Aphidius ervi developing in its host, Acyrthosiphon pisum, parasitized at seven different ages. The parasitoid wing size was used as an estimator of both whole body size and its cellular composition. No size difference was observed in A. ervi adults emerged from aphids 1, 2 or 3 days old at parasitization. Body size then increased in A. ervi emerged from hosts older at parasitization. Body size values as related to host age at parasitization were achieved by adjusting developmental time, developmental rate or both. Parasitoids of similar size, but developed in hosts parasitized at different ages, had different wing cellular composition, while the increase of parasitoid body size was related to a general increase in both cell area and cell number. These results seem to suggest a trade‐off between adult size and developmental time, at least for parasitoids developed at the two extremes of host ages at parasitization, and that A. ervi can reach the same adult size via different trajectories, adapting its ontogenetic processes. Wing shape was typical for all the different parasitoid classes considered and differed strongly between males and females, independent of their size. Parasitoid males (haploids) and females (diploids) did not differ in either cell area or cell number, suggesting a possible sex‐determined dosage compensation in somatic tissue endoreplication. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 439–454.     

Flow cytometric analysis of nuclear DNA content in Musa

 Nuclear genome size variation was studied in Musa acuminata (A genome), Musa balbisiana (B genome) and a range of triploid clones differing in genomic constitution (i.e. the relative number of A and B genomes). Nuclear DNA content was estimated by flow cytometry of nuclei stained by propidium iodide. The A and B genomes of Musa differ in size, the B genome being smaller by 12% on average. No variation in genome size was found among the accessions of M. balbisiana (average genome size 537 Mbp). Small, but statistically significant, variation was found among the subspecies and clones of M. acuminata (ranging from 591 to 615 Mbp). This difference may relate to the geographical origin of the individual accessions. Larger variation in genome size (8.8%) was found among the triploid Musa accessions (ranging from 559 to 613 Mbp). This variation may be due to different genomic constitutions as well as to differences in the size of their A genomes. It is proposed that a comparative analysis of genome size in diploids and triploids may be helpful in identifying putative diploid progenitors of cultivated triploid Musa clones. Statistical analysis of data on genome size resulted in a grouping which agreed fairly well with the generally accepted taxonomic classification of Musa. Received: 11 May 1998 / Accepted: 29 September 1998     

Effects of thermal and oxygen conditions during development on cell size in the common rough woodlice Porcellio scaber

During development, cells may adjust their size to balance between the tissue metabolic demand and the oxygen and resource supply: Small cells may effectively absorb oxygen and nutrients, but the relatively large area of the plasma membrane requires costly maintenance. Consequently, warm and hypoxic environments should favor ectotherms with small cells to meet increased metabolic demand by oxygen supply. To test these predictions, we compared cell size (hindgut epithelium, hepatopancreas B cells, ommatidia) in common rough woodlice (Porcellio scaber) that were developed under four developmental conditions designated by two temperatures (15 or 22°C) and two air O₂ concentrations (10% or 22%). To test whether small‐cell woodlice cope better under increased metabolic demand, the CO₂ production of each woodlouse was measured under cold, normoxic conditions and under warm, hypoxic conditions, and the magnitude of metabolic increase (MMI) was calculated. Cell sizes were highly intercorrelated, indicative of organism‐wide mechanisms of cell cycle control. Cell size differences among woodlice were largely linked with body size changes (larger cells in larger woodlice) and to a lesser degree with oxygen conditions (development of smaller cells under hypoxia), but not with temperature. Developmental conditions did not affect MMI, and contrary to predictions, large woodlice with large cells showed higher MMI than small woodlice with small cells. We also observed complex patterns of sexual difference in the size of hepatopancreatic cells and the size and number of ommatidia, which are indicative of sex differences in reproductive biology. We conclude that existing theories about the adaptiveness of cell size do not satisfactorily explain the patterns in cell size and metabolic performance observed here in P. scaber. Thus, future studies addressing physiological effects of cell size variance should simultaneously consider different organismal elements that can be involved in sustaining the metabolic demands of tissue, such as the characteristics of gas‐exchange organs and O₂‐binding proteins.     

The chloroplast and mitochondrial genomes of two Gomphonema parvulum (Bacillariophyta) environmental isolates from South Carolina (United States) and Virginia (United States)

Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata.     

High-throughput sequencing uncover Ficus tikoua Bur. chloroplast genome

Ficus tikoua Bur., called “di guo”, is a very important economic plant. However, we know little on its molecular mechanisms for a long time. In this study, three F. tikoua chloroplast genomes were first obtained through Illumina sequencing. The F. tikoua Bur. cp genomes exhibited a typical circular structure, including a pair of inverted repeats, a small single copy sequence, and a long single copy sequence. More than 100 genes and about 70 ncRNAs (rRNAs, tRNAs, snRNA, snoRNA, etc.) were identified in each cp genomes. Some repeats, including DNA element, long terminal repeat, small RNA, simple repeat and low complexity, were examined in the three complete cp genomes. In addition, phylogeny tree from six Ficus. species and five Morus. species in family Moracea were constructed for clarifying taxonomy. This data can help further the understanding of evolution and phylogenetic relationships in F. tikoua Bur.

     

Effective population size does not predict codon usage bias in mammals

Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (N_e), with selection on CUB operating less efficiently in species with small N_e. Here, we specifically ask whether variation in N_e predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of N_e (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X‐linked genes, and high‐recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in N_e predicts variation in CUB. Second, across six mammalian species with genetic estimates of N_e (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), N_e and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in N_e does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between N_e and CUB.     

Age‐specific maternal effects interact with larval food supply to modulate life history in Coleomegilla maculata

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Repetitive DNA in the automictic fungus <Emphasis Type="Italic">Microbotryum violaceum</Emphasis>

The small genomes of fungi are expected to have little repetitive content other than rDNA genes. Moreover, among asexual or highly selfing lineages, the diversity of repetitive elements is also expected to be very low. However, in the automictic fungus Microbotryum violaceum, a very large proportion of random DNA fragments from the autosomes and the fungal sex chromosomes are repetitive in nature, either as retrotransposon or helicase sequences. Among the retrotransposon sequences, examples were found from each major kind of elements, including copia, gypsy, and non-LTR sequences. The most numerous were copia-like elements, which are believed to be rare in fungi, particularly among basidiomycetes. The many helicase sequences appear to belong to the recently discovered Helitron type of transposable elements. Also, sequences that could not be identified as a known type of gene were also very repetitive within the database of random fragments from M. violaceum. The differentiated pair of fungal sex chromosomes and suppression of recombination may be the major forces determining the highly repetitive content in the small genome of M. violaceum.     

A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?

Genome sizes vary widely among species, but comprehensive explanations for the emergence of this variation have not been validated. Lynch and Conery (2003) hypothesized that genome expansion is maladaptive, and that lineages with small effective population size (N_e) evolve larger genomes than those with large N_e as a consequence of the lowered efficacy of natural selection in small populations. In addition, mating systems likely affect genome size evolution via effects on both N_e and the spread of transposable elements (TEs). We present a comparative analysis of the effects of N_e and mating system on genome size evolution in seed plants. The dataset includes 205 species with monoploid genome size estimates (corrected for recent polyploidy) ranging from 2Cx = 0.3 to 65.9 pg. The raw data exhibited a strong positive relationship between outcrossing and genome size, a negative relationship between N_e and genome size, but no detectable N_e× outcrossing interaction. In contrast, phylogenetically independent contrast analyses found only a weak relationship between outcrossing and genome size and no relationship between N_e and genome size. Thus, seed plants do not support the Lynch and Conery mechanism of genome size evolution. Further work is needed to disentangle contrasting effects of mating systems on the efficacy of selection and TE transmission.