Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.

A Genome-wide hybrid incompatibility landscape between Caenorhabditis briggsae and C. nigoni

Systematic characterization of ẖybrid incompatibility (HI) between related species remains the key to understanding speciation. The genetic basis of HI has been intensively studied in Drosophila species, but remains largely unknown in other species, including nematodes, which is mainly due to the lack of a sister species with which C. elegans can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has opened up the possibility of dissecting the genetic basis of HI in nematode species. However, the paucity of dominant and visible marker prevents the efficient mapping of HI loci between the two species. To elucidate the genetic basis of speciation in nematode species, we first generated 96 chromosomally integrated GFP markers in the C. briggsae genome and mapped them into the defined locations by PCR and Next-Generation Sequencing (NGS). Aided by the marker, we backcrossed the GFP-associated C. briggsae genomic fragments into C. nigoni for at least 15 generations and produced 111 independent introgressions. The introgression fragments cover most of the C. briggsae genome. We finally dissected the patterns of HI by scoring the embryonic lethality, larval arrest, sex ratio and male sterility for each introgression line, through which we identified pervasive HI loci and produced a genome-wide landscape of HI between the two nematode species, the first of its type for any non-Drosophila species. The HI data not only provided insights into the genetic basis of speciation, but also established a framework for the possible cloning of HI loci between the two nematode species. Furthermore, the data on hybrids confirmed Haldane’s rule and suggested the presence of a large X effect in terms of fertility between the two species. Importantly, this work opens a new avenue for studying speciation genetics between nematode species and allows parallel comparison of the HI with that in Drosophila and other species.

Hybrid incompatibility (HI) has been intensively studied among Drosophila species, but remains largely unknown in other species. Model organism is a species of choice for the HI study because these species provide sophisticated molecular and genetic tools for illustrating mechanism underlying a given HI. C. elegans as a model organism contributed little to the field due to the lack of a sister species with which it can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has made it possible to study the HI between nematode species. However, the paucity of molecular and genetic tools in both species inhibits their use in such studies. To empower the use of this species pair in HI studies, we first created a collection of fluorescent markers over the C. briggsae genome to facilitate the directional introduction of the marker-associated C. briggsae genomic fragments into the C. nigoni background. We next mapped the marker insertion sites and introduced the markers into C. nigoni by repeated crossings. Finally, we generated a genome-wide HI landscape between the two species by scoring the HI phenotypes of their hybrid progeny. The study not only provides an invaluable resource for the molecular cloning of HI loci between C. briggsae and C. nigoni, but also permits comparative analysis of speciation genetics between nematode and other species.

Mutations in Caenorhabditis briggsae identify new genes important for limiting the response to EGF signaling during vulval development

Studies of vulval development in the nematode C. elegans have identified many genes that are involved in cell division and differentiation processes. Some of these encode components of conserved signal transduction pathways mediated by EGF, Notch, and Wnt. To understand how developmental mechanisms change during evolution, we are doing a comparative analysis of vulva formation in C. briggsae, a species that is closely related to C. elegans. Here, we report 14 mutations in 7 Multivulva (Muv) genes in C. briggsae that inhibit inappropriate division of vulval precursors. We have developed a new efficient and cost-effective gene mapping method to localize Muv mutations to small genetic intervals on chromosomes, thus facilitating cloning and functional studies. We demonstrate the utility of our method by determining molecular identities of three of the Muv genes that include orthologs of Cel-lin-1 (ETS) and Cel-lin-31 (Winged-Helix) of the EGF-Ras pathway and Cel-pry-1 (Axin), of the Wnt pathway. The remaining four genes reside in regions that lack orthologs of known C. elegans Muv genes. Inhibitor studies demonstrate that the Muv phenotype of all four new genes is dependent on the activity of the EGF pathway kinase, MEK. One of these, Cbr-lin(gu167), shows modest increase in the expression of Cbr-lin-3/EGF compared to wild type. These results argue that while Cbr-lin(gu167) may act upstream of Cbr-lin-3/EGF, the other three genes influence the EGF pathway downstream or in parallel to Cbr-lin-3. Overall, our findings demonstrate that the genetic program underlying a conserved developmental process includes both conserved and divergent functional contributions.

Fundamentals of Comparative Genome Analysis in Caenorhabditis Nematodes

The genome of the nematode Caenorhabditis elegans was the first of any animal to be sequenced completely, and it remains the "gold standard" for completeness and annotations. Even before the C. elegans genome was completed, however, biologists began examining the generality of its features in the genomes of other Caenorhabditis species. With many such genomes now sequenced and available via WormBase, C. elegans researchers are often confronted with how to interpret comparative genomic data. In this article, we present practical approaches to addressing several common issues, including possible sources of error in homology annotations, the often complex relationships between sequence similarity, orthology, paralogy, and gene family evolution, the impact of sexual mode on genome assemblies and content, and the determination and use of synteny as a tool.

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes

As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution. C. briggsae CSR-1-associated small RNAs that we identified by immunoprecipitation-small RNA sequencing overlap with 22G-RNAs depleted in cbr-csr-1 RNAi-treated worms. By comparing 22G-RNAs and target genes between species, we defined a set of CSR-1 target genes with conserved germline expression, enrichment in operons and more slowly evolving coding sequences than other genes, along with a small group of evolutionarily labile targets. We demonstrate that the association of CSR-1 with chromatin is preserved, and show that depletion of cbr-csr-1 leads to chromosome segregation defects and embryonic lethality. This first comparative characterization of a small RNA pathway in Caenorhabditis establishes a conserved nuclear role for CSR-1 and highlights its key role in germline gene regulation across multiple animal species.

Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes

Given the large number of RNA-binding proteins and regulatory RNAs within genomes, posttranscriptional regulation may be an underappreciated aspect of cis-regulatory evolution. Here, we focus on nematode germ cells, which are known to rely heavily upon translational control to regulate meiosis and gametogenesis. GLD-1 belongs to the STAR-domain family of RNA-binding proteins, conserved throughout eukaryotes, and functions in Caenorhabditis elegans as a germline-specific translational repressor. A phylogenetic analysis across opisthokonts shows that GLD-1 is most closely related to Drosophila How and deuterostome Quaking, both implicated in alternative splicing. We identify messenger RNAs associated with C. briggsae GLD-1 on a genome-wide scale and provide evidence that many participate in aspects of germline development. By comparing our results with published C. elegans GLD-1 targets, we detect nearly 100 that are conserved between the two species. We also detected several hundred Cbr-GLD-1 targets whose homologs have not been reported to be associated with C. elegans GLD-1 in either of two independent studies. Low expression in C. elegans may explain the failure to detect most of them, but a highly expressed subset are strong candidates for Cbr-GLD-1-specific targets. We examine GLD-1-binding motifs among targets conserved in C. elegans and C. briggsae and find that most, but not all, display evidence of shared ancestral binding sites. Our work illustrates both the conservative and the dynamic character of evolution at the posttranslational level of gene regulation, even between congeners.

Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes

Because there is considerable variation in gene expression even between closely related species, it is clear that gene regulatory mechanisms evolve relatively rapidly. Because primary sequence conservation is an unreliable proxy for functional conservation of cis-regulatory elements, their assessment must be carried out in vivo. We conducted a survey of cis-regulatory conservation between C. elegans and closely related species C. briggsae, C. remanei, C. brenneri, and C. japonica. We tested enhancers of eight genes from these species by introducing them into C. elegans and analyzing the expression patterns they drove. Our results support several notable conclusions. Most exogenous cis elements direct expression in the same cells as their C. elegans orthologs, confirming gross conservation of regulatory mechanisms. However, the majority of exogenous elements, when placed in C. elegans, also directed expression in cells outside endogenous patterns, suggesting functional divergence. Recurrent ectopic expression of different promoters in the same C. elegans cells may reflect biases in the directions in which expression patterns can evolve due to shared regulatory logic of coexpressed genes. The fact that, despite differences between individual genes, several patterns repeatedly emerged from our survey, encourages us to think that general rules governing regulatory evolution may exist and be discoverable.

Sex-biased gene expression and evolution of the x chromosome in nematodes

Studies of X chromosome evolution in various organisms have indicated that sex-biased genes are nonrandomly distributed between the X and autosomes. Here, to extend these studies to nematodes, we annotated and analyzed X chromosome gene content in four Caenorhabditis species and in Pristionchus pacificus. Our gene expression analyses comparing young adult male and female mRNA-seq data indicate that, in general, nematode X chromosomes are enriched for genes with high female-biased expression and depleted of genes with high male-biased expression. Genes with low sex-biased expression do not show the same trend of X chromosome enrichment and depletion. Combined with the observation that highly sex-biased genes are primarily expressed in the gonad, differential distribution of sex-biased genes reflects differences in evolutionary pressures linked to tissue-specific regulation of X chromosome transcription. Our data also indicate that X dosage imbalance between males (XO) and females (XX) is influential in shaping both expression and gene content of the X chromosome. Predicted upregulation of the single male X to match autosomal transcription (Ohno's hypothesis) is supported by our observation that overall transcript levels from the X and autosomes are similar for highly expressed genes. However, comparison of differentially located one-to-one orthologs between C. elegans and P. pacificus indicates lower expression of X-linked orthologs, arguing against X upregulation. These contradicting observations may be reconciled if X upregulation is not a global mechanism but instead acts locally on a subset of tissues and X-linked genes that are dosage sensitive.

Centromere identity from the DNA point of view

The centromere is a chromosomal locus responsible for the faithful segregation of genetic material during cell division. It has become evident that centromeres can be established literally on any DNA sequence, and the possible synergy between DNA sequences and the most prominent centromere identifiers, protein components, and epigenetic marks remains uncertain. However, some evolutionary preferences seem to exist, and long-term established centromeres are frequently formed on long arrays of satellite DNAs and/or transposable elements. Recent progress in understanding functional centromere sequences is based largely on the high-resolution DNA mapping of sequences that interact with the centromere-specific histone H3 variant, the most reliable marker of active centromeres. In addition, sequence assembly and mapping of large repetitive centromeric regions, as well as comparative genome analyses offer insight into their complex organization and evolution. The rapidly advancing field of transcription in centromere regions highlights the functional importance of centromeric transcripts. Here, we comprehensively review the current state of knowledge on the composition and functionality of DNA sequences underlying active centromeres and discuss their contribution to the functioning of different centromere types in higher eukaryotes.

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Background

Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species.

Results

Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains.

Conclusions

The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.

Rapid creation of forward-genetics tools for C. briggsae using TALENs: lessons for nonmodel organisms

Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to facilitate both approaches in Caenorhabditis nematodes. First, by combining golden gate cloning and TALEN technology, we can induce frameshifting mutations in any gene. Second, by combining this approach with bioinformatics we can predict and create the resources needed for forward genetic analysis in species like Caenorhabditis briggsae. Although developing genetic model organisms used to require years to isolate marker mutations, balancers, and tools, with TALENs, these reagents can now be produced in months. Furthermore, the analysis of nonsense mutants in related model organisms allows a directed approach for making these markers and tools. When used together, these methods could simplify the adaptation of other organisms for forward and reverse genetics.

WormBase: Annotating many nematode genomes

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

Reproductive isolation in Caenorhabditis briggsae: Dysgenic interactions between maternal- and zygotic-effect loci result in a delayed development phenotype

In sexual species, speciation occurs through the accumulation of genetic barriers to gene flow. In Caenorhabditis briggsae, one such barrier impedes gene flow between temperate strains and the tropical AF16 strain. Up to 20% of F2 progeny derived from crosses of AF16 to strains from the temperate clade exhibit a delayed development phenotype. This phenotype, which results from dysgenic interactions between maternal- and zygyotic-effect loci, causes a ~21% decrease in the intrinsic growth rate. The maternal-effect requires contributions from both parental genotypes. The dysgenic maternal-effect allele appears to be fixed in the temperate clade of C. briggsae and appears to have arisen between 700 and 15,000 y ago. The dysgenic zygotic allele appears to be present only in AF16 and also may be of recent origin.

Cell- and subunit-specific mechanisms of CNG channel ciliary trafficking and localization in C. elegans

Primary cilia are ubiquitous sensory organelles that concentrate transmembrane signaling proteins essential for sensing environmental cues. Mislocalization of crucial ciliary signaling proteins, such as the tetrameric cyclic nucleotide-gated (CNG) channels, can lead to cellular dysfunction and disease. Although several cis- and trans-acting factors required for ciliary protein trafficking and localization have been identified, whether these mechanisms act in a protein- and cell-specific manner is largely unknown. Here, we show that CNG channel subunits can be localized to discrete ciliary compartments in individual sensory neurons in C. elegans, suggesting that channel composition is heterogeneous across the cilium. We demonstrate that ciliary localization of CNG channel subunits is interdependent on different channel subunits in specific cells, and identify sequences required for efficient ciliary targeting and localization of the TAX-2 CNGB and TAX-4 CNGA subunits. Using a candidate gene approach, we show that Inversin, transition zone proteins, intraflagellar transport motors and a MYND-domain protein are required to traffic and/or localize CNG channel subunits in both a cell- and channel subunit-specific manner. We further find that TAX-2 and TAX-4 are relatively immobile in specific sensory cilia subcompartments, suggesting that these proteins undergo minimal turnover in these domains in mature cilia. Our results uncover unexpected diversity in the mechanisms that traffic and localize CNG channel subunits to cilia both within and across cell types, highlighting the essential contribution of this process to cellular functions.

Genomic signatures of selection at linked sites: unifying the disparity among species

Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and the removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive differences in linked selection among species--including roles for selective sweeps being 'hard' or 'soft'--and the concealing effects of demography and confounding genomic variables. We advocate targeted studies of closely related species to unify our understanding of how selection and linkage interact to shape genome evolution.

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs), and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep-sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei, and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. We identified 54 miRNA families that are conserved in each of the four species, as well as numerous miRNAs that are species-specific or shared between only two or three species. Despite a lack of conservation of individual piRNAs and siRNAs, many of the features of each pathway are conserved between the different species. We show that the genomic distribution of 26G siRNAs and the tendency for piRNAs to cluster is conserved between C. briggsae and C. elegans. We also show that, in each species, 26G siRNAs trigger stage-specific secondary siRNA formation. piRNAs in each species also trigger secondary siRNA formation from targets containing up to three mismatches. Finally, we show that the production of male- and female-specific piRNAs is conserved in all four species, suggesting distinct roles for piRNAs in male and female germlines.

Dispersal and gene flow in free-living marine nematodes

Dispersal and gene flow determine connectivity among populations, and can be studied through population genetics and phylogeography. We here review the results of such a framework for free-living marine nematodes. Although field experiments have illustrated substantial dispersal in nematodes at ecological time scales, analysis of the genetic diversity illustrated the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart. In contrast, only little genetic structuring was observed within an estuary (<50 km), indicating that these small scale fluctuations in genetic differentiation are stabilized over deeper time scales through extensive gene flow. Interestingly, nematode species with contrasting life histories (extreme colonizers vs persisters) or with different habitat preferences (algae vs sediment) show similar, low genetic structuring. Finally, historical events have shaped the genetic pattern of marine nematodes and show that gene flow is restricted at large geographical scales. We also discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity.

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis

In most eukaryotes, the kinetochore protein complex assembles at a single locus termed the centromere to attach chromosomes to spindle microtubules. Holocentric chromosomes have the unusual property of attaching to spindle microtubules along their entire length. Our mechanistic understanding of holocentric chromosome function is derived largely from studies in the nematode Caenorhabditis elegans, but holocentric chromosomes are found over a broad range of animal and plant species. In this review, we describe how holocentricity may be identified through cytological and molecular methods. By surveying the diversity of organisms with holocentric chromosomes, we estimate that the trait has arisen at least 13 independent times (four times in plants and at least nine times in animals). Holocentric chromosomes have inherent problems in meiosis because bivalents can attach to spindles in a random fashion. Interestingly, there are several solutions that have evolved to allow accurate meiotic segregation of holocentric chromosomes. Lastly, we describe how extensive genome sequencing and experiments in nonmodel organisms may allow holocentric chromosomes to shed light on general principles of chromosome segregation.

Three genes involved in the oxidative burst are closely linked in the genome of the snail, Biomphalaria glabrata

Allelic variation at the Cu-Zn superoxide dismutase (SOD1) locus has been shown to be associated with resistance of the snail, Biomphalaria glabrata, to infection by the trematode parasite, Schistosoma mansoni. SOD1 catalyses the production of hydrogen peroxide, a known cytotoxic component of the oxidative burst used in defence against pathogens. In our laboratory population of B. glabrata, the most resistant allele at SOD1 is over-expressed relative to the other two alleles. Because hydrogen peroxide also causes oxidative stress on host tissues, we hypothesised that over-expression of SOD1 might be compensated by epistatic interactions with other loci involved in oxidation-reduction (redox) pathways. Catalase, peroxiredoxins and glutathione peroxidases all degrade hydrogen peroxide. We tested whether alleles at each of these loci were in linkage disequilibrium with SOD1 in our population, as might be expected given strong epistatic selection. We found that SOD1, catalase (CAT) and a peroxiredoxin locus (PRX4) are in strong linkage disequilibrium in our population. We also found that these loci are tightly linked, within 1-2cM of each other, which explains the high linkage disequilibrium. This result raises the possibility that there is a linked cluster of redox genes, and perhaps other defence-relevant genes, in the B. glabrata genome. Whether epistatic interactions for fitness actually exist among these loci still needs to be tested. However the close physical linkage among SOD1, PRX4 and CAT, and subsequent high disequilibrium, makes such interactions a plausible hypothesis.

Genetic control of vulval development in Caenorhabditis briggsae

The nematode Caenorhabditis briggsae is an excellent model organism for the comparative analysis of gene function and developmental mechanisms. To study the evolutionary conservation and divergence of genetic pathways mediating vulva formation, we screened for mutations in C. briggsae that cause the egg-laying defective (Egl) phenotype. Here, we report the characterization of 13 genes, including three that are orthologs of Caenorhabditis elegans unc-84 (SUN domain), lin-39 (Dfd/Scr-related homeobox), and lin-11 (LIM homeobox). Based on the morphology and cell fate changes, the mutants were placed into four different categories. Class 1 animals have normal-looking vulva and vulva-uterine connections, indicating defects in other components of the egg-laying system. Class 2 animals frequently lack some or all of the vulval precursor cells (VPCs) due to defects in the migration of P-cell nuclei into the ventral hypodermal region. Class 3 animals show inappropriate fusion of VPCs to the hypodermal syncytium, leading to a reduced number of vulval progeny. Finally, class 4 animals exhibit abnormal vulval invagination and morphology. Interestingly, we did not find mutations that affect VPC induction and fates. Our work is the first study involving the characterization of genes in C. briggsae vulva formation, and it offers a basis for future investigations of these genes in C. elegans.

Temperature-dependent behaviours are genetically variable in the nematode Caenorhabditis briggsae

Temperature-dependent behaviours in Caenorhabditis elegans, such as thermotaxis and isothermal tracking, are complex behavioural responses that integrate sensation, foraging and learning, and have driven investigations to discover many essential genetic and neural pathways. The ease of manipulation of the Caenorhabditis model system also has encouraged its application to comparative analyses of phenotypic evolution, particularly contrasts of the classic model C. elegans with C. briggsae. And yet few studies have investigated natural genetic variation in behaviour in any nematode. Here we measure thermotaxis and isothermal tracking behaviour in genetically distinct strains of C. briggsae, further motivated by the latitudinal differentiation in C. briggsae that is associated with temperature-dependent fitness differences in this species. We demonstrate that C. briggsae performs thermotaxis and isothermal tracking largely similar to that of C. elegans, with a tendency to prefer its rearing temperature. Comparisons of these behaviours among strains reveal substantial heritable natural variation within each species that corresponds to three general patterns of behavioural response. However, intraspecific genetic differences in thermal behaviour often exceed interspecific differences. These patterns of temperature-dependent behaviour motivate further development of C. briggsae as a model system for dissecting the genetic underpinnings of complex behavioural traits.

A method for rapid and simultaneous mapping of genetic loci and introgression sizes in nematode species

Caenorhabditis briggsae is emerging as an attractive model organism not only in studying comparative biology against C. elegans, but also in developing novel experimentation avenues. In particular, recent identification of a new Caenorhabditis species, C. sp.9 with which it can mate and produce viable progeny provides an opportunity for studying the genetics of hybrid incompatibilities (HI) between the two. Mapping of a specific HI locus demands repeated backcrossing to get hold of the specific genomic region underlying an observed phenotype. To facilitate mapping of HI loci between C. briggsae and C. sp.9, an efficient mapping method and a genetic map ideally consisting of dominant markers are required for systematic introgression of genomic fragments between the two species. We developed a fast and cost-effective method for high throughput mapping of dominant loci with resolution up to 1 million bps in C. briggsae. The method takes advantage of the introgression between C. briggsae and C. sp.9 followed by PCR genotyping using C. briggsae specific primers. Importantly, the mapping results can not only serve as an effective way for estimating the chromosomal position of a genetic locus in C. briggsae, but also provides size information for the introgression fragment in an otherwise C. sp.9 background. In addition, it also helps generate introgression line as a side-product that is invaluable for the subsequent mapping of HI loci. The method will greatly facilitate the construction of a genetic map consisting of dominant markers and pave the way for systematic isolation of HI loci between C. briggsae and C. sp.9 which has so far not been attempted between nematode species. The method is designed for mapping of a dominant allele, but can be easily adapted for mapping of any other type of alleles in any other species if introgression between a sister species pair is feasible.

An improved allele-specific PCR primer design method for SNP marker analysis and its application

BACKGROUND

Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3'end (SNP site) have been used in AS-PCR. However, for one SNP site, nine possible mismatches can be generated among the three bases and how to select the right one to increase primer specificity is still a challenge.

RESULTS

In this study, different from the previous reports which used a limited quantity of primers randomly (several or dozen pairs), we systematically investigated the effects of mismatch base pairs, mismatch sites and SNP types on primer specificity with 2071 primer pairs, which were designed based on SNPs from Brassica oleracea 01-88 and 02-12. According to the statistical results, we (1) found that the primers designed with SNP (A/T), in which the mismatch (CA) in the 3rd nucleotide from the 3' end, had the highest allele-specificity (81.9%). This information could be used when designing primers from a large quantity of SNP sites; (2) performed the primer design principle which forms the one and only best primer for every SNP type. This is never reported in previous studies. Additionally, we further identified its availability in rapeseed (Brassica napus L.) and sesame (Sesamum indicum). High polymorphism percent (75%) of the designed primers indicated it is a general method and can be applied in other species.

CONCLUSION

The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods. The high allele-specific efficiency of the SNP primer allows the feasibility for low- to moderate- throughput SNP analyses and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops.

RNA-seq analysis of the C. briggsae transcriptome

Curation of a high-quality gene set is the critical first step in genome research, enabling subsequent analyses such as ortholog assignment, cis-regulatory element finding, and synteny detection. In this project, we have reannotated the genome of Caenorhabditis briggsae, the best studied sister species of the model organism Caenorhabditis elegans. First, we applied a homology-based gene predictor genBlastG to annotate the C. briggsae genome. We then validated and further improved the C. briggsae gene annotation through RNA-seq analysis of the C. briggsae transcriptome, which resulted in the first validated C. briggsae gene set (23,159 genes), among which 7347 genes (33.9% of all genes with introns) have all of their introns confirmed. Most genes (14,812, or 68.3%) have at least one intron validated, compared with only 3.9% in the most recent WormBase release (WS228). Of all introns in the revised gene set (103,083), 61,503 (60.1%) have been confirmed. Additionally, we have identified numerous trans-splicing leaders (SL1 and SL2 variants) in C. briggsae, leading to the first genome-wide annotation of operons in C. briggsae (1105 operons). The majority of the annotated operons (564, or 51.0%) are perfectly conserved in C. elegans, with an additional 345 operons (or 31.2%) somewhat divergent. Additionally, RNA-seq analysis revealed over 10 thousand small-size assembly errors in the current C. briggsae reference genome that can be readily corrected. The revised C. briggsae genome annotation represents a solid platform for comparative genomics analysis and evolutionary studies of Caenorhabditis species.

Recent progress on the identity and characterization of factors that shape gene organization during eukaryotic evolution

Comparative genomics has identified regions of chromosomes susceptible to participate in rearrangements that modify gene order and genome architecture. Additionally, despite the high levels of genome rearrangement, unusually large regions that remain unaffected have also been uncovered. Functional constraints, such as long-range enhancers or local coregulation of neighboring genes, are thought to explain the maintenance of gene order (i.e., collinearity conservation) among distantly related species since the disruption of these protected regions would cause detrimental misregulation of gene expression. Local enrichment of certain genetic elements in regions of conserved collinearity has been used to support the existence of regulatory-based constraints, although the evidence is largely circumstantial. Indeed, a mechanism of chromosome evolution based only on the existence of fragile regions (i.e., those more susceptible to breaks) can also give rise to extended collinearity conservation, making it difficult to determine whether conserved gene organization is actually caused by functional constraints. Chromosome engineering coupled with genome wide expression profiling and phenotypic assays can provide unambiguous evidence for the presence of functional constraints acting on particular genomic regions. We have recently used this integrated approach to evaluate the presence and nature of putative constraints acting on one of the largest chromosomal regions conserved across nine species of Drosophila. We propose that regulatory-based constraints might not suffice to explain the maintenance of gene organization of some chromosome domains over evolutionary time.

Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes

It is important to understand the forces that shape the size and evolutionary histories of gene families. Here, we investigated the evolution of non–protein-coding RNA genes in the genomes of Caenorhabditis nematodes. We specifically focused on nested arrangements, that is, cases in which an RNA gene is entirely contained in an intron of another gene. Comparing these arrangements between species simplifies the inference of orthology and, therefore, of evolutionary fates of nested genes. Two distinct patterns are evident in the data. Genes encoding small nuclear RNAs (snRNAs) and transfer RNAs form large families, which have persisted since before the common ancestor of Metazoa. Yet, individual genes die relatively rapidly, with few orthologs having survived since the divergence of Caenorhabditis elegans and Caenorhabditis briggsae. In contrast, genes encoding small nucleolar RNAs (snoRNAs) are either single-copy or form small families. Individual snoRNAs turn over at a relatively slow rate—most C. elegans genes have clearly identifiable orthologs in C. briggsae. We also found that in Drosophila, genes from larger snRNA families die at a faster rate than their counterparts from single-gene families. These results suggest that a relationship between family size and the rate of gene turnover may be a general feature of genome evolution.

Developmental genetics of secretory vesicle acidification during Caenorhabditis elegans spermatogenesis

Secretory vesicles are used during spermatogenesis to deliver proteins to the cell surface. In Caenorhabditis elegans, secretory membranous organelles (MO) fuse with the plasma membrane to transform spermatids into fertilization-competent spermatozoa. We show that, like the acrosomal vesicle of mammalian sperm, MOs undergo acidification during development. Treatment of spermatids with the V-ATPase inhibitor bafilomycin blocks both MO acidification and formation of functional spermatozoa. There are several spermatogenesis-defective mutants that cause defects in MO morphogenesis, including spe-5. We determined that spe-5, which is on chromosome I, encodes one of two V-ATPase B paralogous subunits. The spe-5 null mutant is viable but sterile because it forms arrested, multi-nucleate spermatocytes. Immunofluorescence with a SPE-5-specific monoclonal antibody shows that SPE-5 expression begins in spermatocytes and is found in all subsequent stages of spermatogenesis. Most SPE-5 is discarded into the residual body during spermatid budding, but a small amount remains in budded spermatids where it localizes to MOs as a discrete dot. The other V-ATPase B subunit is encoded by vha-12, which is located on the X chromosome. Usually, spe-5 mutants are self-sterile in a wild-type vha-12 background. However, an extrachromosomal transgene containing wild-type vha-12 driven by its own promoter allows spe-5 mutant hermaphrodites to produce progeny, indicating that VHA-12 can at least partially substitute for SPE-5. Others have shown that the X chromosome is transcriptionally silent in the male germline, so expression of the autosomally located spe-5 gene ensures that a V-ATPase B subunit is present during spermatogenesis.

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

BACKGROUND

Many metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation.

RESULTS

We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c.

CONCLUSIONS

A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes.

Nematode and snail metallothioneins

Metallobiologists have, at large, neglected soil dwelling invertebrates; exceptions are the nematode (Caenorhabditis elegans) and snails (Helix pomatia and Cantareus aspersus). This review aims to compare and contrast the molecular, protein and cellular mechanisms of the multifunctional nematode and snail metallothioneins (MTs). The C. elegans genome contains two MT genes, mtl-1, which is constitutively expressed in the pharynx and likely to act as an essential and/or toxic metal sensor, and mtl-2, which plays a negligible role under normal physiological conditions but is strongly induced (as mtl-1) in intestinal cells upon metal exposure. It has been possible to follow the intricate phenotypic responses upon the knockdown/knockout of single and multiple MT isoforms and we have started to decipher the multifunctional role of C. elegans MTs. The snails have contributed to our understanding regarding MT evolution and diversity, structure and metal-specific functionality. The H. pomatia and C. aspersus genomes contain at least three MT isoform genes. CdMT is responsible for cadmium detoxification, CuMT is involved in copper homeostasis and Cd/CuMT is a putative ancestral MT possibly only of minor importance in metal metabolism. Further investigations of nematode, snail and other invertebrate MTs will allow the development of alternative biomarker approaches and lead to an improved understanding of metallobiology, protein evolution and toxicogenomics.

Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.

Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals

The compact genome of fugu (Takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of fugu and anchored the scaffolds of the assembly to the 22 chromosomes of fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.fugu-sg.org/). The integrated genome map revealed a higher recombination rate in fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of fugu. We used the extended assembly to explore recent rearrangement events in the lineages of fugu, Tetraodon, and medaka and compared them with rearrangements in three mammalian (human, mouse, and opossum) lineages. Between the two pufferfishes, fugu has experienced fewer chromosomal rearrangements than Tetraodon. The gene order is more highly conserved in the three teleosts than in mammals largely due to a lower rate of interchromosomal rearrangements in the teleosts. These results provide new insights into the distinct patterns of genome evolution between teleosts and mammals. The consolidated genome map and the genetic map of fugu are valuable resources for comparative genomics of vertebrates and for elucidating the genetic basis of the phenotypic diversity of ~25 species of Takifugu that evolved within the last 5 My.

Proteome of the Caenorhabditis elegans oocyte

Oocytes were purified from the temperature-sensitive fertilization-defective fer-1(b232ts) mutant of the nematode Caenorhabditis elegans and used for comprehensive mass spectrometric analysis. Using stringent criteria, 1165 C. elegans proteins were identified; at lower stringency, an additional 288 proteins were identified. We validate the high degree of sample purity and evaluate several possible sources of bias in the proteomic data. We compare the classes of proteins identified in the current oocyte proteome with protein classes identified in our previously determined oocyte transcriptome. The oocyte proteome appears enriched in proteins likely to be needed immediately upon fertilization, whereas the transcriptome appears enriched in molecules and processes needed later in embryogenesis. The current study provides fundamental background information for future more detailed studies of oocyte biology.

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

Background

High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer). Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits.

Results

A second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb) in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease.

Conclusions

We constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic improvement of growth performance, and it also provides critical resource for future genome sequence assembly and comparative genomics studies on the evolution of fish genomes.

Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift

The emergence of multigene families has been hypothesized as a major contributor to the evolution of complex traits and speciation. To help understand how such multigene families arose and diverged during plant evolution, we examined the phylogenetic relationships of F-Box (FBX) genes, one of the largest and most polymorphic superfamilies known in the plant kingdom. FBX proteins comprise the target recognition subunit of SCF-type ubiquitin-protein ligases, where they individually recruit specific substrates for ubiquitylation. Through the extensive analysis of 10,811 FBX loci from 18 plant species, ranging from the alga Chlamydomonas reinhardtii to numerous monocots and eudicots, we discovered strikingly diverse evolutionary histories. The number of FBX loci varies widely and appears independent of the growth habit and life cycle of land plants, with a little as 198 predicted for Carica papaya to as many as 1350 predicted for Arabidopsis lyrata. This number differs substantially even among closely related species, with evidence for extensive gains/losses. Despite this extraordinary inter-species variation, one subset of FBX genes was conserved among most species examined. Together with evidence of strong purifying selection and expression, the ligases synthesized from these conserved loci likely direct essential ubiquitylation events. Another subset was much more lineage specific, showed more relaxed purifying selection, and was enriched in loci with little or no evidence of expression, suggesting that they either control more limited, species-specific processes or arose from genomic drift and thus may provide reservoirs for evolutionary innovation. Numerous FBX loci were also predicted to be pseudogenes with their numbers tightly correlated with the total number of FBX genes in each species. Taken together, it appears that the FBX superfamily has independently undergone substantial birth/death in many plant lineages, with its size and rapid evolution potentially reflecting a central role for ubiquitylation in driving plant fitness.

Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae

BACKGROUND

Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial dysfunction in aging processes has been the lack of model systems with relevant, naturally occurring mitochondrial genetic variation. Toward the goal of developing such a model system, we studied natural variation in life history, metabolic, and aging phenotypes as it relates to levels of a naturally-occurring heteroplasmic mitochondrial ND5 deletion recently discovered to segregate among wild populations of the soil nematode, Caenorhabditis briggsae. The normal product of ND5 is a central component of the mitochondrial electron transport chain and integral to cellular energy metabolism.

RESULTS

We quantified significant variation among C. briggsae isolates for all phenotypes measured, only some of which was statistically associated with isolate-specific ND5 deletion frequency. We found that fecundity-related traits and pharyngeal pumping rate were strongly inversely related to ND5 deletion level and that C. briggsae isolates with high ND5 deletion levels experienced a tradeoff between early fecundity and lifespan. Conversely, oxidative stress resistance was only weakly associated with ND5 deletion level while ATP content was unrelated to deletion level. Finally, mean levels of reactive oxygen species measured in vivo showed a significant non-linear relationship with ND5 deletion level, a pattern that may be driven by among-isolate variation in antioxidant or other compensatory mechanisms.

CONCLUSIONS

Our findings suggest that the ND5 deletion may adversely affect fitness and mitochondrial functioning while promoting aging in natural populations, and help to further establish this species as a useful model for explicit tests of hypotheses in aging biology and mitochondrial genetics.

Specialized chromosomes and their uses in Caenorhabditis elegans

Research on Caenorhabditis elegans involves the use of a wide range of genetic and molecular tools consisting of chromosomal material captured and modified for specific purposes. These "specialized chromosomes" come in many forms ranging from relatively simple gene deletions to complex rearrangements involving endogenous chromosomes as well as transgenic constructs. In this chapter, we describe the specialized chromosomes that are available in C. elegans, their origins, practical considerations, and methods for generation and evaluation. We will summarize their uses for biological studies, and their contribution to our knowledge about chromosome biology.

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

BACKGROUND

Although Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known.

RESULTS

We determined the genomic regions associated with the nuclear transmembrane protein LEM-2 in mixed-stage C. elegans embryos via chromatin immunoprecipitation. Large regions of several megabases on the arms of each autosome were associated with LEM-2. The center of each autosome was mostly free of such interactions, suggesting that they are largely looped out from the nuclear membrane. Only the left end of the X chromosome was associated with the nuclear membrane. At a finer scale, the large membrane-associated domains consisted of smaller subdomains of LEM-2 associations. These subdomains were characterized by high repeat density, low gene density, high levels of H3K27 trimethylation, and silent genes. The subdomains were punctuated by gaps harboring highly active genes. A chromosome arm translocated to a chromosome center retained its association with LEM-2, although there was a slight decrease in association near the fusion point.

CONCLUSIONS

Local DNA or chromatin properties are the main determinant of interaction with the nuclear membrane, with position along the chromosome making a minor contribution. Genes in small gaps between LEM-2 associated regions tend to be highly expressed, suggesting that these small gaps are especially amenable to highly efficient transcription. Although our data are derived from an amalgamation of cell types in mixed-stage embryos, the results suggest a model for the spatial arrangement of C. elegans chromosomes within the nucleus.

Insights into species divergence and the evolution of hermaphroditism from fertile interspecies hybrids of Caenorhabditis nematodes

The architecture of both phenotypic variation and reproductive isolation are important problems in evolutionary genetics. The nematode genus Caenorhabditis includes both gonochoristic (male/female) and androdioecious (male/hermaprodite) species. However, the natural genetic variants distinguishing reproductive mode remain unknown, and nothing is known about the genetic basis of postzygotic isolation in the genus. Here we describe the hybrid genetics of the first Caenorhabditis species pair capable of producing fertile hybrid progeny, the gonochoristic Caenorhabditis sp. 9 and the androdioecious C. briggsae. Though many interspecies F(1) arrest during embryogenesis, a viable subset develops into fertile females and sterile males. Reciprocal parental crosses reveal asymmetry in male-specific viability, female fertility, and backcross viability. Selfing and spermatogenesis are extremely rare in XX F(1), and almost all hybrid self-progeny are inviable. Consistent with this, F(1) females do not express male-specific molecular germline markers. We also investigated three approaches to producing hybrid hermaphrodites. A dominant mutagenesis screen for self-fertile F(1) hybrids was unsuccessful. Polyploid F(1) hybrids with increased C. briggsae genomic material did show elevated rates of selfing, but selfed progeny were mostly inviable. Finally, the use of backcrosses to render the hybrid genome partial homozygous for C. briggsae alleles did not increase the incidence of selfing or spermatogenesis relative to the F(1) generation. These hybrid animals were genotyped at 23 loci, and significant segregation distortion (biased against C. briggsae) was detected at 13 loci. This, combined with an absence of productive hybrid selfing, prevents formulation of simple hypotheses about the genetic architecture of hermaphroditism. In the near future, this hybrid system will likely be fruitful for understanding the genetics of reproductive isolation in Caenorhabditis.

Temperature-dependent fecundity associates with latitude in Caenorhabditis briggsae

Populations of organisms separated by latitude provide striking examples of local adaptation, by virtue of ecological gradients that correlate with latitudinal position on the globe. Ambient temperature forms one key ecological variable that varies with latitude, and here we investigate its effects on the fecundity of self-fertilizing nematodes of the species Caenorhabditis briggsae that exhibits strong genetically based differentiation in association with latitude. We find that isogenic strains from a Tropical phylogeographic clade have greater lifetime fecundity when reared at extreme high temperatures and lower lifetime fecundity at extreme low temperatures than do strains from a Temperate phylogeographic clade, consistent with adaptation to local temperature regimes. Further, we determine experimentally that the mechanism underlying reduced fecundity at extreme temperatures differs for low versus high temperature extremes, but that the total number of sperm produced by the gonad is unaffected by rearing temperature. Low rearing temperatures result in facultatively reduced oocyte production by hermaphrodites, whereas extreme high temperatures experienced during development induce permanent defects in sperm fertility. Available and emerging genetic tools for this organism will permit the characterization of the evolutionary genetic basis to this putative example of adaptation in latitudinally separated populations.

Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster

BACKGROUND

Accurate identification of synteny blocks is an important step in comparative genomics towards the understanding of genome architecture and expression. Most computer programs developed in the last decade for identifying synteny blocks have limitations. To address these limitations, we recently developed a robust program called OrthoCluster, and an online database OrthoClusterDB. In this work, we have demonstrated the application of OrthoCluster in identifying synteny blocks between the genomes of Caenorhabditis elegans and Caenorhabditis briggsae, two closely related hermaphrodite nematodes.

RESULTS

Initial identification and analysis of synteny blocks using OrthoCluster enabled us to systematically improve the genome annotation of C. elegans and C. briggsae, identifying 52 potential novel genes in C. elegans, 582 in C. briggsae, and 949 novel orthologous relationships between these two species. Using the improved annotation, we have detected 3,058 perfect synteny blocks that contain no mismatches between C. elegans and C. briggsae. Among these synteny blocks, the majority are mapped to homologous chromosomes, as previously reported. The largest perfect synteny block contains 42 genes, which spans 201.2 kb in Chromosome V of C. elegans. On average, perfect synteny blocks span 18.8 kb in length. When some mismatches (interruptions) are allowed, synteny blocks ("imperfect synteny blocks") that are much larger in size are identified. We have shown that the majority (80%) of the C. elegans and C. briggsae genomes are covered by imperfect synteny blocks. The largest imperfect synteny block spans 6.14 Mb in Chromosome X of C. elegans and there are 11 synteny blocks that are larger than 1 Mb in size. On average, imperfect synteny blocks span 63.6 kb in length, larger than previously reported.

CONCLUSIONS

We have demonstrated that OrthoCluster can be used to accurately identify synteny blocks and have found that synteny blocks between C. elegans and C. briggsae are almost three-folds larger than previously identified.

Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae

The combined actions of natural selection, mutation, and recombination forge the landscape of genetic variation across genomes. One frequently observed manifestation of these processes is a positive association between neutral genetic variation and local recombination rates. Two selective mechanisms and/or recombination-associated mutation (RAM) could generate this pattern, and the relative importance of these alternative possibilities remains unresolved generally. Here we quantify nucleotide differences within populations, between populations, and between species to test for genome-wide effects of selection and RAM in the partially selfing nematode Caenorhabditis briggsae. We find that nearly half of genome-wide variation in nucleotide polymorphism is explained by differences in local recombination rates. By quantifying divergence between several reproductively isolated lineages, we demonstrate that ancestral polymorphism generates a spurious signal of RAM for closely related lineages, with implications for analyses of humans and primates; RAM is, at most, a minor factor in C. briggsae. We conclude that the positive relation between nucleotide polymorphism and the rate of crossover represents the footprint of natural selection across the C. briggsae genome and demonstrate that background selection against deleterious mutations is sufficient to explain this pattern. Hill-Robertson interference also leaves a signature of more effective purifying selection in high-recombination regions of the genome. Finally, we identify an emerging contrast between widespread adaptive hitchhiking effects in species with large outcrossing populations (e.g., Drosophila) versus pervasive background selection effects on the genomes of organisms with self-fertilizing lifestyles and/or small population sizes (e.g., Caenorhabditis elegans, C. briggsae, Arabidopsis thaliana, Lycopersicon, human). These results illustrate how recombination, mutation, selection, and population history interact in important ways to shape molecular heterogeneity within and between genomes.

Conserved mechanism of Wnt signaling function in the specification of vulval precursor fates in C. elegans and C. briggsae

The C. elegans hermaphrodite vulva serves as a paradigm for understanding how signaling pathways control organ formation. Previous studies have shown that Wnt signaling plays important roles in vulval development. To understand the function and evolution of Wnt signaling in Caenorhabditis nematodes we focused on C. briggsae, a species that is substantially divergent from C. elegans in terms of the evolutionary time scale yet shares almost identical morphology. We isolated mutants in C. briggsae that display multiple pseudo-vulvae resulting from ectopic VPC induction. We cloned one of these loci and found that it encodes an Axin homolog, Cbr-PRY-1. Our genetic studies revealed that Cbr-pry-1 functions upstream of the canonical Wnt pathway components Cbr-bar-1 (beta-catenin) and Cbr-pop-1(tcf/lef) as well as the Hox target Cbr-lin-39 (Dfd/Scr). We further characterized the pry-1 vulval phenotype in C. briggsae and C. elegans using 8 cell fate markers, cell ablation, and genetic interaction approaches. Our results show that ectopically induced VPCs in pry-1 mutants adopt 2° fates independently of the gonad-derived inductive and LIN-12/Notch-mediated lateral signaling pathways. We also found that Cbr-pry-1 mutants frequently show a failure of P7.p induction. A similar, albeit low penetrant, defect is also observed in C. elegans pry-1 mutants. The genetic analysis of the P7.p induction defect revealed that it was caused by altered regulation of lin-12 and its transcriptional target lip-1 (MAP kinase phosphatase). Thus, our results provide evidence for LIN-12/Notch-dependent and independent roles of Wnt signaling in promoting 2 degrees VPC fates in both nematode species.

A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

BACKGROUND

The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

RESULTS

We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3.

CONCLUSIONS

We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.

The evolutionary dynamics of operon distributions in eukaryote genomes

Genes in nematode and ascidian genomes frequently occur in operons--multiple genes sharing a common promoter to generate a polycistronic primary transcript--and such genes comprise 15-20% of the coding genome for Caenorhabditis elegans and Ciona intestinalis. Recent work in nematodes has demonstrated that the identity of genes within operons is highly conserved among species and that the unifying feature of genes within operons is that they are expressed in germline tissue. However, it is generally unknown what processes are responsible for generating the distribution of operon sizes across the genome, which are composed of up to eight genes per operon. Here we investigate several models for operon evolution to better understand their abundance, distribution of sizes, and evolutionary dynamics over time. We find that birth-death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes and generate predictions about the number of monocistronic, nonoperon genes that likely participate in the birth-death process. This theory, and applications to C. elegans and Ciona, motivates several new and testable hypotheses about eukaryote operon evolution.