What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence

The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively. Including additional sequences located on other linkage groups a total of 12 Mb were subjected to a manual gene extraction and annotation process. The genome comprises a small number of repetitive elements, a low degree of segmental duplications and very few paralogous genes. The analysis of the 3218 identified open reading frames provides a first overview of the protein equipment of a filamentous fungus. Significantly, N.crassa possesses a large variety of metabolic enzymes including a substantial number of enzymes involved in the degradation of complex substrates as well as secondary metabolism. While several of these enzymes are specific for filamentous fungi many are shared exclusively with prokaryotes.     

Bird-nest puzzle: can the study of unisexual flowers such as cucumber solve the problem of plant sex determination?

Unisexual flower development has long been used as a model system to understand the mechanism of plant sex determination. However, based on our investigation of the mechanisms regulating the development of unisexual cucumber flowers, we have realized that understanding how organ development is inhibited may not necessarily reveal how an organ is formed. We refer to this problem as a "bird-nest puzzle," meaning one cannot understand how a bird lays and hatches its eggs by understanding how its nest is ruined. To understand the biological significance of unisexual flowers, we reexamine the original meaning of sex and its application in plants. Additionally, we propose that the fundamental biological advantage for the selection and maintenance of unisexual flowers during evolution is to promote cross pollination.     

Why become speckled? Ontogeny and function of speckling in Shark Bay bottlenose dolphins (Tursiops sp.)1

To date, color patterns have been used to assess cetacean age and taxonomic status, but few studies have determined precise correlates of coloration with known age or investigated its function. Here, we examine the ontogeny of speckling in 88 bottlenose dolphins (Tursiops sp.) in Shark Bay, Australia, of known age, tracked from birth to age 34. Ventral speckles first appear in the genital area at a mean age of 10.2 ± 0.35 yr (range = 7.6–12.7 yr). Throughout their life span, speckles increase in number and density, particularly along the ventral and lateral sides. The timing of speckle onset does not significantly differ by sex but is related to sexual maturity in females. The age of speckle onset in the genital area correlates with the age of first known parturition. In terms of speckle function, we discuss two hypotheses commonly proffered to explain color variation, concealment, and communication. Concealment from predators or prey is unlikely to explain speckle development in Shark Bay Tursiops because the onset occurs long after peak predation risk and initial hunting success (at 3 mo of age). We suggest that speckle patterns offer reliable cues on reproductive status and/or condition and could, thus, serve a communicative or some other function.     

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.     

Discordance Between Spatial Distributions of Y-Chromosomal and Mitochondrial Haplotypes in African Green Monkeys (Chlorocebus spp.): A Result of Introgressive Hybridization or Cryptic Diversity?

Introgressive hybridization may cause substantial discordances among phylogenies based on different genetic markers. Such discordances have been found in diverse mammal species including primates. A recent study of mitochondrial DNA (mtDNA) revealed several poly- and paraphyletic relationships in African green monkeys (Chlorocebus), suggesting contemporary and/or ancient introgressive hybridization among almost all parapatric species of the genus. However, mtDNA analyses alone do not allow us to draw conclusions concerning introgression events. In this study we analyzed two Y chromosomal (Y-chr) markers for 30 African green monkey samples and compared the resulting genetic relationships to those based on published mtDNA data. In line with the results for mtDNA, we found no Y-chr evidence of hypothesized hybridization among Chlorocebus sabaeus and C. tantalus in the northern part of the contact zone in West Africa, and we found two distinct and distantly related Y-chr haplotypes within the range of C. tantalus, suggesting possible cryptic genetic diversity rather than ancient introgressive hybridization in this species. In contrast, Y-chr data revealed monophyletic relationships within Chlorocebus pygerythrus from East Africa, suggesting that mtDNA paraphylies found in this species are most likely to be the result of ancient introgressive hybridization and subsequent cytonuclear extinction of an earlier taxon. Our results accentuate the importance of analyzing sex chromosomal data in addition to mtDNA to obtain more information on the potential outcomes of hybridization with respect to genetic and species diversity. Analysis of more diverse nuclear marker sets is needed to obtain a more complete picture of the African green monkey evolution.     

Bird–nest puzzle: can the study of unisexual flowers such as cucumber solve the problem of plant sex determination?

Unisexual flower development has long been used as a model system to understand the mechanism of plant sex determination. However, based on our investigation of the mechanisms regulating the development of unisexual cucumber flowers, we have realized that understanding how organ development is inhibited may not necessarily reveal how an organ is formed. We refer to this problem as a “bird–nest puzzle,” meaning one cannot understand how a bird lays and hatches its eggs by understanding how its nest is ruined. To understand the biological significance of unisexual flowers, we reexamine the original meaning of sex and its application in plants. Additionally, we propose that the fundamental biological advantage for the selection and maintenance of unisexual flowers during evolution is to promote cross pollination.     

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.     

Why do dolphins jump? Interpreting the behavioural repertoire of bottlenose dolphins (Tursiops sp.) in Doubtful Sound,New Zealand

Only a limited number of studies have tried to determine the purpose of surface behavioural events performed by dolphins. To date only one study has attempted to aggregate the behavioural events observed in a population in contextual groups using co-occurrence as the grouping factor. In the present study, I tried to characterise the behavioural repertoire of a bottlenose dolphin population (Tursiops sp.) present in Doubtful Sound, New Zealand. I first looked at the relationship between events performed by individuals depending on the behavioural state of their schools. I then assessed the likelihood for events to co-occur. Four main behavioural categories (orientation, travel, social displays and fights) emerged from this analysis. Aerial events (jumps) did not fall into one category, showing that different aerial behaviours play different roles. Moreover, it appears that dolphins used side-flopping and upside-down lobtailing to communicate motivation. Side-flops occurred when the focal schools finished a behavioural bout and started to travel, while upside-down lobtails occurred when the focal schools instigated a behavioural bout after travelling. This non-vocal communication can take place over a few meters to hundreds of meters. Having signals that are effective over very short ranges avoids unwanted signalling to prey, predators or conspecifics.     

Cryptic Species? Patterns of Maternal and Paternal Gene Flow in Eight Neotropical Bats

Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th) intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of the genetic species concept but demonstrate that estimates of mitochondrial diversity alone do not accurately represent gene flow in these species and that contact/hybrid zones must be explored to evaluate reproductive isolation.     

Does sex of children matter? Implications for fertility in Pakistan

Preference for children of either sex is considered a constraint on fertility decline as it induces many couples to keep adding on surviving children in the hope of having a desired sex composition of children. However, preferences for children of a particular sex may differ in relation to demographic and socioeconomic characteristics of women, traditional values and cultural practices, such as propagating a family name, providing economic advantages, and obtaining a medium of social and economic security in times of illness, unemployment and old age. Utilizing the Pakistan Integrated Household Survey (2001-02), this paper aims at investigating the existence of sex preference and examines sex preference differentials by different attributes of women in Pakistan. The results reveal that there is a desire to have another child in the presence of all children of one sex, either sons or daughters. The desire to have a son with only or mostly daughters, however, is stronger than the desire to have a daughter with only or mostly sons. This behaviour will retard fertility decline unless there is a shift in the desire to have children of both sexes in Pakistan.     

Dendrochronological evidence of cockchafer (Melolontha sp.) outbreaks in subfossil tree-trunks from Tovačov (CZ Moravia)

In dendrochronological dating, we encounter the trouble that some samples cannot be dated due to the occurrence of anomalies in the tree-ring series. When dating subfossil wood for the extension of existing master chronologies, this may be an especially unwanted circumstance as subfossil wood is scarce and each sample is valuable. In Moravia (Czech Republic) outbreaks of the cockchafer (Melolontha sp.) used to appear with a disastrous effect on agricultural crops, and, for a dendrochronologist, on samples of wood to be dated. Oak ring width reduction caused by cockchafer induced defoliation can superimpose climate induced growth variations and may complicate dating of historical or subfossil samples. For this study, 33 samples of sub-fossil trunks were assessed; 19 of which were attacked by cockchafer. For comparison, we analysed a total of nine living oak trees from the forest district Strá?nice-Vracov, recently attacked by the cockchafer. Occurrence of the cockchafer was reported there in 1999, 2003 and 2007.We found clear growth patterns with cyclic narrow rings every 4 years. This allowed us to create an artificial curve expressing the recurring cycles of cockchafer outbreaks which assisted us in the detection of the same pattern in subfossil tree growth. The tree-ring series of the attacked living oak stand as well as the 19 individual tree-ring series from subfossil oak trunks could not be dated using standard chronologies and showed a high resemblance to the cockchafer life cycle. Additionally, we found out that the living oak stand was attacked in 1983, 1987, 1991 and 1995 as well. The results support the hypothesis that the periodical reduction observed in tree-rings at regular increments is caused by cockchafer infestation. This evidence is further supported by characteristic anatomical features in early wood. A mean tree-ring series was created from the individual tree-ring series of subfossil oaks even though radiocarbon dating showed completely different ages of samples. This means that the affected tree-ring series cannot be used for dendrochronological dating and dendroclimatological analyses. These series cannot be used without preceding mathematical and statistical modification.     

The ‘A’ genome donor of Eleusine coracana (L.) Gaertn. (Gramineae)

Summary In an attempt to discover A and B genome donor(s) to finger millet, Eleusine coracana, or its progenitor species, E. africana (both allotetraploid 2n=4x=36), five diploid species, E. Indica, E. Floccifolia, E. multiflora, E. tristachya and E. intermedia, were crossed to finger millet and its progenitor taxon. Crosses were successful only with E. coracana. Three combinations of triploid hybrids E. coracana x E. indica, E. coracana x E. floccifolia, and E. coracana x E. multiflora were obtained and analysed. Meiotic behaviour was perfectly normal in parental species. The regular number of 18 bivalents in E. coracana, 9 bivalents in E. indica, E. intermedia, E. tristachya and E. floccifolia and 8 bivalents in E. multiflora were invariably noticed. In E. coracana x E. indica hybrids a mean chromosome pairing of 8.84_I+8.80_II+0.03_III+0.10_IV per cell was found. About 86.5% of the cells showed the typical 9_I+9_II configuration, suggesting that E. indica (AA) is one of the diploid genome donors to cultivated species E. coracana. A mean chromosome pairing of 11.08_I+7.63_II+0.16_III+0.04_IV per cell was found in E. coracana x E. floccifolia hybrids. Two to ten bivalents and varying numbers of univalents were seen in 55% of the cells. About 45% of the cells showed the 9_I+9_II configuration. Various evidence suggests that perennial E. floccifolia is a primitive member of the A genome group of Eleusine species, and it may not be a genome donor to E. coracana. In E. coracana x E. multiflora hybrids (2n=26) mean chromosome pairing of 21.45_I+1.97_II+0.13_III+0.04_IV per cell was found. About 91% of the cells were observed to have 20–26 univalents. Only a small percentage of the cells contained bivalents or multivalents. This pairing behaviour indicates that E. multiflora lacks genomic homology with the A or B genome of E. coracana. Genomically E. multiflora is a distinct species and a genomic symbol of C is assigned to it. Identification of the B genome donor species to cultivated millet. E. coracana remains elusive.     

Is genome downsizing associated with diversification in polyploid lineages of Veronica?

The study of genome size evolution in a phylogenetic context in related polyploid and diploid lineages can help us to understand the advantages and disadvantages of genome size changes and their effect on diversification. Here, we contribute 199 new DNA sequences and a nearly threefold increase in genome size estimates in polyploid and diploid Veronica (Plantaginaceae) (to 128 species, c. 30% of the genus) to provide a comprehensive baseline to explore the effect of genome size changes. We reconstructed internal transcribed spacer (ITS) and trnL‐trnL‐trnF phylogenetic trees and performed phylogenetic generalized least squares (PGLS), ancestral character state reconstruction, molecular dating and diversification analyses. Veronica 1C‐values range from 0.26 to 3.19 pg. Life history is significantly correlated with 1C‐value, whereas ploidy and chromosome number are strongly correlated with both 1C‐ and 1Cx‐values. The estimated ancestral Veronica 1Cx‐value is 0.65 pg, with significant genome downsizing in the polyploid Southern Hemisphere subgenus Pseudoveronica and two Northern Hemisphere subgenera, and significant genome upsizing in two diploid subgenera. These genomic downsizing events are accompanied by increased diversification rates, but a ‘core shift’ was only detected in the rate of subgenus Pseudoveronica. Polyploidy is important in the evolution of the genus, and a link between genome downsizing and polyploid diversification and species radiations is hypothesized. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 243–266.     

Sex differences in the meiotic behavior of an XX sex chromosome pair in males and females of the mole vole Ellobius tancrei: turning an X into a Y chromosome?

Chromosoma - Sex determination in mammals is usually provided by a pair of chromosomes, XX in females and XY in males. Mole voles of the genus Ellobius are exceptions to this rule. In Ellobius...     

The effect of temperature on sex ratio in the isopod Porcellionides pruinosus: Environmental sex determination or a by-product of cytoplasmic sex determination?

The sex ratios of the progenies of woodlice Porcellionides pruinosus (Crustacea, Isopoda) raised at different temperatures were studied. Females from three French populations sampled in the wild produced highly female-biased broods at 20°C and male-biased broods above 30°C. The effect of high temperature was not due to selective mortality of females. Sex determination was thus sensitive to temperature in P. pruinosus. We also found an interpopulation variability of sex ratio thermosensitivity and a weak inheritance of male-biased sex ratios at high temperatures. Samples taken from a wild population throughout the year showed that while the thermal conditions required for changes in the sex ratio occurred, there was no significant variation in the sex ratio. On the other hand, almost all the females and many males in the four populations studied harboured intracytoplasmic bacteria. These maternally inherited symbionts belong to the genus Wolbachia and are known to possess a feminizing effect. While in other arthropods Wolbachia are destroyed at high temperatures, the symbionts of P. pruinosus were detected by a PCR procedure whatever the rearing temperatures. In light of these results, we propose that the thermosensitivity of sex determination in P. pruinosus could reflect the removal of the cytoplasmic effect on sex determination rather than environmental sex determination sensu stricto. The reduction in the amount of bacteria (but not their entire elimination), or the inhibition of bacterial metabolism, may be responsible for sex ratio variations relating to temperature. The incomplete inheritance of male-biased sex ratios at high temperatures might reflect a selection of thermo-tolerant bacterial strains.     

Structural variability in the genome of phage ?H of Halobacterium halobium

Summary The partially circularly permuted, terminally redundant structure of the DNA of phage H has been confirmed by a cleavage map for the restriction enzymes PstI, ClaI, BglII, HindIII, and, partially, BamHI.Six variants of phage H have been isolated from 71 single plaques. Their genomes differ by several insertions, a deletion, and an inversion of a DNA segment with a minimal length of 11 kb. The inversion occurs with high frequency in variants carrying at the flanks of the invertible DNA in verted repeats of a 1.8 kb DNA element which shares sequence homology with the DNA of H. halobium and may be involved in the extreme variability of its genome.     

Will knowledge of human genome variation result in changing cancer paradigms?

Our incomplete understanding of carcinogenesis may be a significant reason why some cancer mortality rates are still increasing. This lack of understanding is likely due to a research approach that relies heavily on genetic comparison between cancerous and non-cancerous tissues and cells, which has led to the identification of genes of cancer proliferation rather than differentiation. Recent observations showing that a tremendous degree of natural human genetic variation occurs are likely to lead to a shift in the basic paradigms of cancer genetics, in that there is a need to consider both the nature of the genes involved, and the idea that not every genetic variation identified in these genes may be associated with carcinogenesis. Based on studies using LCM and micro-genetic analyses, we propose that significant cancer initiating events may take place during the very early stages of development of cancer-susceptible tissues and that using such techniques might greatly help us in our understanding of carcinogenesis.