Sequencing the Oxytricha trifallax macronuclear genome: a pilot project

The Codon Usage Bias Analysis of Free-Living Ciliates' Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction of Stylonychia lemnae

Ciliates represent higher unicellular animals, and several species are also important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome in ciliates can not only promote a better understanding of the genetic mode and evolution history of these organisms but also help optimize codons to improve the gene editing efficiency of model ciliates. In this study, macronuclear genome sequences of nine free-living ciliates were analyzed with CodonW software to calculate the following indices: the guanine-cytosine content (GC); the frequency of the nucleotides U, C, A, and G at the third position of codons (U3s, C3s, A3s, G3s); the effective number of codons (ENC); the correlation between GC at the first and second positions (GC12); the frequency of the nucleotides G + C at the third position of synonymous codons (GC3s); the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, neutrality plot analysis, and correlation analysis were performed to explore the factors that influence codon preference. The results showed that the GC contents in nine ciliates' MAC genomes were lower than 50% and appeared AT-rich. The base compositions of GC12 and GC3s are markedly distinct and the codon usage pattern and evolution of ciliates are affected by genetic mutation and natural selection. According to the synonymous codon analysis, the codons of most ciliates ended with A or U and eight codons were the general optimal codons of nine ciliates. A clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) expression vector of Stylonychia lemnae was constructed by optimizing the macronuclear genome codon and was successfully used to knock out the Adss gene. This is the first such extensive investigation of the MAC genome CUB of ciliates and the initial successful application of the CRISPR/Cas9 technique in free-living ciliates.

Telomere repeats and macronuclear DNA organization in the soil ciliate Kahliella matisi (Ciliophora, Hypotricha)

To better understand the structure of macronuclear chromosomes in ciliates, the organization of macronuclear DNA was investigated in the hypotrich Kahliella matisi. Total DNA of K. matisi separated by agarose gel electrophoresis showed continuous smear ranging in size from ∼500bp to ∼15kb. This fragmentation was found to be due to the presence of gene-sized macronuclear chromosomes. The sequence analysis of four randomly cloned macronuclear chromosomes showed that K. matisi telomeres consist of 5'-dC4A4-3' repeats and carry one or two open reading frames. The transcription unit was found to be flanked with non-coding AT rich 5' leader and 3' trailer. No consensus transcription-regulatory sequences were identified in 5' leader and only one of analyzed gene-sized chromosomes showed the presence of conserved poly(A) addition signal sequence in 3' trailer. All ORFs showed highest relatedness to Oxytricha trifallax macronuclear chromosomes with conserved exon/intron structure. Sequence comparisons indicate that macronuclear chromosome organization is at least partially conserved in ciliates.

Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway

To establish which meiosis genes are present in ciliates, and to look for clues as to which recombination pathways may be treaded by them, four genomes were inventoried for 11 meiosis-specific and 40 meiosis-related genes. We found that the set of meiosis genes shared by Tetrahymena thermophila, Paramecium tetraurelia, Ichthyophthirius multifiliis, and Oxytricha trifallax is consistent with the prevalence of a Mus81-dependent class II crossover pathway that is considered secondary in most model eukaryotes. There is little evidence for a canonical class I crossover pathway that requires the formation of a synaptonemal complex (SC). This gene inventory suggests that meiotic processes in ciliates largely depend on mitotic repair proteins for executing meiotic recombination. We propose that class I crossovers and SCs were reduced sometime during the evolution of ciliates. Consistent with this reduction, we provide microscopic evidence for the presence only of degenerate SCs in Stylonychia mytilus. In addition, lower nonsynonymous to synonymous mutation rates of some of the meiosis genes suggest that, in contrast to most other nuclear genes analyzed so far, meiosis genes in ciliates are largely evolving at a slower rate than those genes in fungi and animals.

Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology

Oxytricha trifallax - an established model organism for studying genome rearrangements, chromosome structure, scrambled genes, RNA-mediated epigenetic inheritance, and other phenomena - has been the subject of a nomenclature controversy for several years. Originally isolated as a sibling species of O. fallax, O. trifallax was reclassified in 1999 as Sterkiella histriomuscorum, a previously identified species, based on morphological similarity. The proper identification of O. trifallax is crucial to resolve in order to prevent confusion in both the comparative genomics and the general scientific communities. We analyzed nine conserved nuclear gene sequences between the two given species and several related ciliates. Phylogenetic analyses suggest that O. trifallax and a bona fide S. histriomuscorum have accumulated significant evolutionary divergence from each other relative to other ciliates such that they should be unequivocally classified as separate species. We also describe the original isolation of O. trifallax, including its comparison to O. fallax, and we provide criteria to identify future isolates of O. trifallax.

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control

Background

Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism.

Results

We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio.

Conclusions

Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rearranged genome that expresses all genes required for growth and asexual reproduction. In some ciliates including Oxytricha, the macronuclear genome is particularly extreme, consisting of thousands of tiny 'nanochromosomes', each of which usually contains only a single gene. Because the organism itself identifies and isolates most of its genes on single-gene nanochromosomes, nanochromosome structure could facilitate the discovery of unusual genes or gene classes, such as ncRNA genes. Using a draft Oxytricha genome assembly and a custom-written protein-coding genefinding program, we identified a subset of nanochromosomes that lack any detectable protein-coding gene, thereby strongly enriching for nanochromosomes that carry ncRNA genes. We found only a small proportion of non-coding nanochromosomes, suggesting that Oxytricha has few independent ncRNA genes besides homologs of already known RNAs. Other than new members of known ncRNA classes including C/D and H/ACA snoRNAs, our screen identified one new family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs.

Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa

Euplotes focardii is a marine ciliated protozoan discovered in the Ross Sea near Terra Nova Bay, Antarctica. This organism is strictly psychrophilic, survives and reproduces optimally at 4-5 °C, and has a genome rich in A/T base pairs. Like other ciliated protozoans, Euplotes spp. are characterized by nuclear dimorphism: 1) the germline micronucleus contains the entire genome as large chromosomes; and 2) the somatic macronucleus (∼50 megabases, or 5% of the micronuclear genome) contains small linear DNA nanochromosomes [1-12 kilobases], each of which constitutes a single genetic unit. These characteristics make E. focardii an ideal model for genome-level analysis to understand the evolutionary mechanisms that determine the adaptation of organisms to cold environments. Here we describe two examples that are controlled by phylogenetically appropriate comparison with mesophilic and psychrotolerant Euplotes species: 1) the genes and encoded proteins of the E. focardii tubulin superfamily, including α-, β-, and γ-tubulins; and 2) the genes of the heat-shock protein (Hsp) 70 family. The tubulins provide particular insight into protein-level structural changes that are likely to facilitate microtubule nucleation and polymerization in an energy poor environment. By contrast, the hsp70 genes of E. focardii and of its psychrotolerant relative E. nobilii reveal adaptive alterations in the regulation of gene expression in the cold. The unique characteristics of the E. focardii genome and the results that we present here argue strongly for a concerted effort to characterize the relatively low complexity macronuclear genome of this psychrophilic organism.

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns

BACKGROUND

Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement.

RESULTS

We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21-29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway.

CONCLUSION

The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.

The pathway to detangle a scrambled gene

Background

Programmed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interrupt coding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and extensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20–30% of the genes are estimated to be scrambled in the germline micronucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangements are therefore critical for development.

Methodology/Principal Findings

To understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during assembly of different scrambled genes in two related organisms in a developmental time-course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways.

Conclusions/Significance

This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of a hidden layer of errors, absent from the mature macronucleus but present during development, also underscores the need for repair or screening of incorrectly-assembled DNA molecules.

Mirror-imaged doublets of Tetmemena pustulata: implications for the development of left-right asymmetry

Ciliated protozoa possess cellular axes reflected in the arrangement of their ciliature. Upon transverse fission, daughter cells develop an identical ciliary pattern, ensuring perpetuation of the cellular phenotype. Experimentally manipulated cells can be induced to form atypical phenotypes, capable of intraclonal propagation and regeneration after encystment. One such phenotype in the ciliate Tetmemena pustulata (formerly Stylonychia pustulata) is the mirror-imaged doublet. These cells possess two distinct sets of ciliature, juxtaposed on the surfaces in mirror image symmetry, with a common anterior-posterior axis. We have examined whether individual ciliary components of Tetmemena mirror-image doublets are mirror imaged. Ultrastructural analysis indicates that despite global mirror imaging of the ciliature, detailed organization of the membranelles is reversed in the mirror-image oral apparatus (OA), such that the ciliary effective stroke propels food away from the OA. Assembly of compound ciliary structures of both OAs starts out identically, but as the structures associated with the mirror-image OA continue to form, the new set of membranelles undergoes a 180 degrees planar rotation on the ventral surface relative to the same structures in the typical OA. The overall symmetry of the OA thus appears to be separable from the more localized assembly of individual basal bodies. True mirror imagery of the membranelles would require new enantiomorphic forms of the individual ciliary components, particularly the basal bodies, which is never observed. These observations suggest a mechanistic hypothesis with implications for the development of left-right asymmetry not only in ciliates, but perhaps also in development of left-right asymmetry in general.

Variation in macronuclear genome content of three ciliates with extensive chromosomal fragmentation: a preliminary analysis

The genome architecture of ciliates, including features such as nuclear dualism and large-scale genome rearrangements, impacts gene and genome evolution in these organisms. To better understand the structure of macronuclear chromosomes in ciliates with extensively processed chromosomes, a sample of complete macronuclear chromosomes was sequenced from three ciliate species: Metopus es (Class [Cl]: Armophorea), Nyctotherus ovalis (Cl: Armophorea), and Chilodonella uncinata (Cl: Phyllopharyngea). By cloning whole macronuclear chromosomes into a plasmid vector, we generated nine clones from each of M. es and C. uncinata, and 37 clones from N. ovalis. Analysis of these macronuclear chromosomes provides insight into the evolution of genome features such as chromosome content, gene structure, and genetic code. Phylogenetic patterns can be found in telomere structure and codon usage, which are both more similar in M. es and N. ovalis than C. uncinata. In addition, we provide evidence of lateral transfer of a bacterial endo-beta-mannanase gene onto a M. es chromosome and report the discovery of a 42-bp conserved sequence motif within N. ovalis untranslated regions.

A PCR-Based Method to Distinguish the Sibling Species Stylonychia mytilus and Stylonychia lemnae (Ciliophora, Spirotrichea) Using Isocitrate Dehydrogenase Gene Sequences

A differentiation, based on morphological characters, between Stylonychia mytilus and Stylonychia lemnae is very difficult, especially for non-specialists. These two sibling species were considered as one species, S. mytilus, until detailed cytological and genetic studies could show the existence of two genetically isolated varieties. Further morphological and biochemical analyses verified the separation and finally in 1983 a new species S. lemnae was described. The examination of several isoenzymes revealed unambiguous differences in the banding pattern of isocitrate dehydrogenase (IDH) between these two species. Therefore, the IDH gene of 30 isolates of S. lemnae and S. mytilus coming from various regions all over the world were amplified and sequenced. The sequence analyses revealed intraspecific as well as interspecific substitutions, which were used for the development of species-specific PCR primers for both species. Application of these species-specific primer pairs now allows a very easy and clear identification of both sibling species.

A General Coverage Theory for Shotgun DNA Sequencing

The classical theory of shotgun DNA sequencing accounts for neither the placement dependencies that are a fundamental consequence of the forward-reverse sequencing strategy, nor the edge effect that arises for small to moderate-sized genomic targets. These phenomena are relevant to a number of sequencing scenarios, including large-insert BAC and fosmid clones, filtered genomic libraries, and macro-nuclear chromosomes. Here, we report a model that considers these two effects and provides both the expected value of coverage and its variance. Comparison to methyl-filtered maize data shows significant improvement over classical theory. The model is used to analyze coverage performance over a range of small to moderately-sized genomic targets. We find that the read pairing effect and the edge effect interact in a non-trivial fashion. Shorter reads give superior coverage per unit sequence depth relative to longer ones. In principle, end-sequences can be optimized with respect to template insert length; however, optimal performance is unlikely to be realized in most cases because of inherent size variation in any set of targets. Conversely, single-stranded reads exhibit roughly the same coverage attributes as optimized end-reads. Although linking information is lost, single-stranded data should not pose a significant assembly liability if the target represents predominantly low-copy sequence. We also find that random sequencing should be halted at substantially lower redundancies than those now associated with larger projects. Given the enormous amount of data generated per cycle on pyro-sequencing instruments, this observation suggests devising schemes to split each run cycle between twoor more projects. This would prevent over-sequencing and would further leverage the pyrosequencing method.

Interconversion of germline-limited and somatic DNA in a scrambled gene

Ciliates have a somatic and a germline nucleus; after sexual conjugation a new somatic nucleus forms from the new zygotic germline nucleus. Formation of the somatic nucleus involves precise elimination of a large portion of DNA sequences from the germline. Here we compare the architecture of the germline and somatic versions of the actin I gene in two geographically isolated strains of Stylonychia lemnae. We show that the structure of the germline gene is surprisingly mercurial, with the distinction between germline-limited and somatic sequences variable over the course of evolution. This is, to our knowledge, the first example of evolutionary swapping of retained versus deleted sequences during ciliate development, with sequences deleted during development that are specifically retained in another strain.

Conserved linkage of two genes on the same macronuclear chromosome in spirotrichous ciliates

Macronuclear chromosomes of spirotrichous ciliates are mainly "nanochromosomes" containing only a single gene. We identified a two-gene chromosome in the spirotrich Sterkiella histriomuscorum (formerly Oxytricha trifallax) which, unlike other characterized two-gene molecules, contains reading frames oriented tail to tail. These are homologs of ribosomal protein L29 (RPL29) and cyclophilin. We found that both genes are transcribed, with their polyadenylation sites on opposite strands separated by only 135 bp. Furthermore, both genes in S. histriomuscorum are present only on one macronuclear chromosome and do not occur alone or linked to other genes. The corresponding micronuclear locus is fragmented into three nonscrambled gene segments (MDSs), separated by two noncoding segments (IESs). We also found that these two genes are linked on a macronuclear chromosome, similarly arranged tail to tail, in the three spirotrichs Stylonychia lemnae, Uroleptus sp., and Holosticha sp.. In addition, single-gene macronuclear chromosomes containing only the RPL29 gene were detected in the earlier diverged Holosticha and Uroleptus. These observations suggest a possible evolutionary trend towards loss of chromosomal breakage between these two genes. This study is the first to examine gene linkage in the macronucleus of several spirotrichs and may provide insight into the evolution of multi-gene macronuclear chromosomes and chromosomal fragmentation in spirotrichs.

A new scrambled gene in the ciliate Uroleptus

In the germline micronucleus of spirotrichous ciliates, the gene segments, or macronuclear destined sequences (MDSs), that give rise to the somatic macronucleus are interrupted by internal eliminated sequences (IESs). For some genes, the MDSs are not arranged sequentially, but rather are scrambled, in the micronucleus. Three scrambled genes have been extensively studied in many species: actin I, alpha-telomere binding protein, and DNA polymerase alpha. However, in the past decade, no new scrambled genes have been reported, and the prevalence of scrambled genes is still an important question. To screen for scrambled genes, we completely sequenced 11 macronuclear chromosomes in the spirotrich Uroleptus sp., and then pursued their micronuclear organization. This allowed us to identify new scrambled genes, which also display novel features. In this study we describe one of these newly discovered scrambled genes. This gene, tentatively named USG1 (Unknown Scrambled Gene 1), encodes a putative protein of 1016 aa. While the function of this protein product is not clear, dN/dS calculated from the two alleles suggests the encoded protein is under purifying selection. USG1 consists of 16 germline MDSs, of which 14 are located on one locus. The other locus, which is at least 3 kb away from the main locus, contains two scrambled MDSs separated by a nonscrambled IES. Curiously, one MDS and its outgoing (3') pointer (direct repeat) overlap intron splice sites, indicating that these DNA sequences may be under dual (or multiple) constraints. Our findings identify a new scrambled gene in the micronuclear genome of a spirotrichous ciliate, and suggest that even more complicated structures may be present.

Gene structure of the ciliate Sterkiella histriomuscorum based on a combined analysis of DNA and cDNA sequences from 21 macronuclear chromosomes

Macronuclear deoxyribonucleic acid (DNA) in hypotrichous ciliates consists of a set of linear molecules ranging in size from 0.5 to several tens of kilobases and typically carrying a single gene. Each minichromosome is present at a ploidy of >or=1,000 per macronucleus. These molecules are known as gene-sized molecules. Multigene molecules are also present, but are still poorly described. In analyzing the encystment-excystment cycle of Sterkiella histriomuscorum, we have characterized a set of 21 macronuclear molecules both at the DNA and complementary DNA (cDNA) levels. On a total of 23 validated coding sequences, we mapped the 5' and 3' untranslated regions for a subset of 10 and 18 transcripts, respectively. A combination of DNA and cDNA data allows us to precisely determine several structural features of macronuclear chromosomes, such as the organization of multigene molecules, an intron content higher than expected, and a conserved sequence surrounding the initiation transcription site. It also reveals one coding sequence containing a transcribed 10-bp element that displays the characteristic features of internal eliminated sequences (IES). Its presence in a fraction of the minichromosomes carrying this gene raises the possibility of an incomplete IES excision process during the development of the S. histriomuscorum macronucleus.

Extension of Lander-Waterman theory for sequencing filtered DNA libraries

Background

The degree to which conventional DNA sequencing techniques will be successful for highly repetitive genomes is unclear. Investigators are therefore considering various filtering methods to select against high-copy sequence in DNA clone libraries. The standard model for random sequencing, Lander-Waterman theory, does not account for two important issues in such libraries, discontinuities and position-based sampling biases (the so-called "edge effect"). We report an extension of the theory for analyzing such configurations.

Results

The edge effect cannot be neglected in most cases. Specifically, rates of coverage and gap reduction are appreciably lower than those for conventional libraries, as predicted by standard theory. Performance decreases as read length increases relative to island size. Although opposite of what happens in a conventional library, this apparent paradox is readily explained in terms of the edge effect. The model agrees well with prototype gene-tagging experiments for Zea mays and Sorghum bicolor. Moreover, the associated density function suggests well-defined probabilistic milestones for the number of reads necessary to capture a given fraction of the gene space. An exception for applying standard theory arises if sequence redundancy is less than about 1-fold. Here, evolution of the random quantities is independent of library gaps and edge effects. This observation effectively validates the practice of using standard theory to estimate the genic enrichment of a library based on light shotgun sequencing.

Conclusion

Coverage performance using a filtered library is significantly lower than that for an equivalent-sized conventional library, suggesting that directed methods may be more critical for the former. The proposed model should be useful for analyzing future projects.

The evolutionary origin of a complex scrambled gene

Some species of ciliates undergo massive DNA elimination and genome rearrangement to construct gene-sized "chromosomes" in their somatic nucleus. An example is the extensively scrambled DNA polymerase alpha gene that is broken into 48 pieces and distributed over two unlinked loci in Stylonychia. To understand the emergence of this complex phenomenon during evolution, we examined DNA polymerase alpha genes in several earlier diverging species, representing evolutionary intermediates. Mapping these data onto an evolutionary tree suggests that this gene became extensively fragmented and scrambled over evolutionary time through a series of steps, each leading to greater complexity. Our results also suggest a possible mechanism for intron loss by deletion of intron sequences as DNA during development of the somatic nucleus.

Complex germline architecture: two genes intertwined on two loci

The germline micronuclear genome of some ciliated protists can be scrambled, with coding segments disordered relative to the expressed macronuclear genome. Here, we report a surprisingly complex pair of genes that assemble from interwoven segments on two germline loci in the ciliate Uroleptus. This baroque organization requires two scrambled genes to be disentangled from each other from two clusters in the genome, one containing segments 1-2-4-5-6-8-11-13-15-16 and the other 7-9-3-10-12-14, with pieces 1-5 comprising the first gene and 6-16 the second gene. Both genes remain linked in the somatic genome on a 1.5-kb "nanochromosome." This study is the first to reveal that two genes can become scrambled during evolution with their coding segments intertwined. These twin scrambled genes underscore the beauty and exceptions of protist genome architecture, pointing to the critical need for evolutionary biologists to survey protist genomes broadly.

Reciprocal Fusions of Two Genes in the Formaldehyde Detoxification Pathway in Ciliates and Diatoms

During the course of a pilot genome project for the ciliate Oxytricha trifallax, we discovered a fusion gene never before described in any taxa. This gene, FSF1, encodes a putative fusion protein comprising an entire formaldehyde dehydrogenase (FALDH) homolog at one end and an S-formylglutathione hydrolase (SFGH) homolog at the other, two proteins that catalyze serial steps in the formaldehyde detoxification pathway. We confirmed the presence of the Oxytricha fusion gene in vivo and detected transcripts of the full-length fusion gene. A survey of other large-scale sequencing projects revealed a similar fusion protein in a distantly related ciliate, Tetrahymena thermophila, and a possible fusion of these two genes in the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana, but in the reverse order, with the SFGH domain encoded upstream of the FALDH domain. Orthologs of these fusion proteins may be widespread within the ciliates and diatoms.

MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates

Ciliated protozoa have two kinds of nuclei: Macronuclei (MAC) and Micronuclei (MIC). In some ciliate classes, such as spirotrichs, most genes undergo several layers of DNA rearrangement during macronuclear development. Because of such processes, these organisms provide ideal systems for studying mechanisms of recombination and gene rearrangement. Here, we describe a database that contains all spirotrich genes for which both MAC and MIC versions are sequenced, with consistent annotation and easy access to all the features. An interface to query the database is available at http://oxytricha.princeton.edu/dimorphism/database.htm.

Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences

We sequenced and analyzed the subtelomeric regions of 1356 macronuclear "nanochromosomes" of the spirotrichous ciliate Oxytricha trifallax. We show that the telomeres in this species have a length of 20 nt, with minor deviations; there is no correlation between telomere lengths at the two ends of the molecule. A search for open reading frames revealed that the 3' and 5' untranslated regions are short, with a median length of approximately 130 nt, and that surprisingly there are no detectable differences between sequences upstream and downstream of genes. Our results confirm a previously reported purine bias in the first approximately 80 nucleotides of the subtelomeric regions, but with this larger data set we curiously detected a 10 bp periodicity in the bias; we relate this finding to the possible regulatory and structural functions these regions must serve. Palindromic sequences in opposing subtelomeric regions, although present in most sequences, are not statistically significant.