Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.

Lophotrochozoan Zic Genes

Lophotrochozoa is a sister taxon of Ecdysozoa in the Protostomia that includes mollusks, annelids, brachiopods, and platyhelminths. Recent studies have clarified the structure, expression, and roles of lophotrochozoan Zic family genes. Zic genes in oligochaete annelid Tubifex tubifex (freshwater sludge worm) and polychaete annelid Capitella teleta (bristle worm) are commonly expressed in a subset of developing brain and mesoderm derivatives. The latter includes the naïve mesoderm and the associated chaetal sacs in each body segment, although the segmentation processes differ between the two species. Furthermore, in brachiopod Terebratalia transversa (lamp shell), Zic is expressed in the anterior ectodermal domains and mesodermal derivatives, including those associated with the chaetal sacs. This result suggests the common involvement of Zic genes in the development of chaetae, a lophotrochozoan novelty acquired in the course of evolution. In addition, the highly simplified lophotrochozoan Dicyema acuticephalum (dicyemid mesozoan, a cephalopod endoparasite), which lost its gut, nervous system, and muscles during evolution, expresses its Zic genes in hermaphroditic gonads, highlighting the role of Zic genes in germ cell development. The role of Zic in head regeneration was revealed in studies on platyhelminth Schmidtea mediterranea (freshwater planarian). Planarian Zic expression was induced in a subpopulation of neoblasts that includes adult pluripotent stem cells. It is needed for head regeneration and production of an anterior signaling center. Suppression of Wnt-β-catenin signaling underlies Zic-mediated head regeneration, reminiscent of Wnt-β-catenin suppression by vertebrate Zic genes. Taken together, studies on the lophotrochozoan Zic genes are essential to understanding not only the roles of these genes in body plan evolution but also the molecular mechanism underlying adult stem cell regulation.

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell

The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities-if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome. First, we find that Stentor uses the standard genetic code, suggesting that ciliate-specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor's cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.

Distribution bias of the sequence matching between exons and introns in exon joint and EJC binding region in C. elegans

We propose a mechanism that there are matching relations between mRNA sequences and corresponding post-spliced introns, and introns play a significant role in the process of gene expression. In order to reveal the sequence matching features, Smith-Waterman local alignment method is used on C. elegans mRNA sequences to obtain optimal matched segments between exon-exon sequences and their corresponding introns. Distribution characters of matching frequency on exon-exon sequences and sequence characters of optimal matched segments are studied. Results show that distributions of matching frequency on exon-exon junction region have obvious differences, and the exon boundary is revealed. Distributions of the length and matching rate of optimal matched segments are consistent with sequence features of siRNA and miRNA. The optimal matched segments have special sequence characters compared with their host sequences. As for the first introns and long introns, matching frequency values of optimal matched segments with high GC content, rich CG dinucleotides and high λCG values show the minimum distribution in exon junction complex (EJC) binding region. High λCG values in optimal matched segments are main characters in distinguishing EJC binding region. Results indicate that EJC and introns have competitive and cooperative relations in the process of combining on protein coding sequences. Also intron sequences and protein coding sequences do have concerted evolution relations.

Origin of spliceosomal introns and alternative splicing

In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.

Diversity and evolution of spliceosomal systems

The intron-exon structures of eukaryotic nuclear genomes exhibit tremendous diversity across different species. The availability of many genomes from diverse eukaryotic species now allows for the reconstruction of the evolutionary history of this diversity. Consideration of spliceosomal systems in comparative context reveals a surprising and very complex portrait: in contrast to many expectations, gene structures in early eukaryotic ancestors were highly complex and "animal or plant-like" in many of their spliceosomal structures has occurred; pronounced simplification of gene structures, splicing signals, and spliceosomal machinery occurring independently in many lineages. In addition, next-generation sequencing of transcripts has revealed that alternative splicing is more common across eukaryotes than previously thought. However, much alternative splicing in diverse eukaryotes appears to play a regulatory role: alternative splicing fulfilling the most famous role for alternative splicing-production of multiple different proteins from a single gene-appears to be much more common in animal species than in nearly any other lineage.

Spliceosomal intron insertions in genome compacted ray-finned fishes as evident from phylogeny of MC receptors, also supported by a few other GPCRs

BACKGROUND

Insertions of spliceosomal introns are very rare events during evolution of vertebrates and the mechanisms governing creation of novel intron(s) remain obscure. Largely, gene structures of melanocortin (MC) receptors are characterized by intron-less architecture. However, recently a few exceptions have been reported in some fishes. This warrants a systematic survey of MC receptors for understanding intron insertion events during vertebrate evolution.

METHODOLOGY/PRINCIPAL FINDINGS

We have compiled an extended list of MC receptors from different vertebrate genomes with variations in fishes. Notably, the closely linked MC2Rs and MC5Rs from a group of ray-finned fishes have three and one intron insertion(s), respectively, with conserved positions and intron phase. In both genes, one novel insertion was in the highly conserved DRY motif at the end of helix TM3. Further, the proto-splice site MAG↑R is maintained at intron insertion sites in these two genes. However, the orthologs of these receptors from zebrafish and tetrapods are intron-less, suggesting these introns are simultaneously created in selected fishes. Surprisingly, these novel introns are traceable only in four fish genomes. We found that these fish genomes are severely compacted after the separation from zebrafish. Furthermore, we also report novel intron insertions in P2Y receptors and in CHRM3. Finally, we report ultrasmall introns in MC2R genes from selected fishes.

CONCLUSIONS/SIGNIFICANCE

The current repository of MC receptors illustrates that fishes have no MC3R ortholog. MC2R, MC5R, P2Y receptors and CHRM3 have novel intron insertions only in ray-finned fishes that underwent genome compaction. These receptors share one intron at an identical position suggestive of being inserted contemporaneously. In addition to repetitive elements, genome compaction is now believed to be a new hallmark that promotes intron insertions, as it requires rapid DNA breakage and subsequent repair processes to gain back normal functionality.

Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences

The oomycetes, a distinct phylogenetic lineage of fungus-like microorganisms, are heterokonts (stramenopiles) belonging to the supergroup Chromalveolata. Although the complete genomic sequences of a number of oomycetes have been reported, little information regarding the introns therein is available. Here, we investigated the introns of Phytophthora sojae, a pathogen that causes soybean root and stem rot, by a comparative analysis of genomic sequences and expressed sequence tags. A total of 4013 introns were identified, of which 96.6% contained canonical splice sites. The P. sojae genome possessed features distinct from other organisms at 5' splice sites, polypyrimidine tracts, branch sites, and 3' splice sites. Diverse repeating sequences, ranging from 2 to 10 nucleotides in length, were found at more than half of the intron-exon boundaries. Furthermore, 122 genes underwent alternative splicing. These data indicate that P. sojae has unique splicing mechanisms, and recognition of those mechanisms may lead to more accurate predictions of the location of introns in P. sojae and even other oomycete species.

Dicyemid's dilemma: structure versus genes. The unorthodox structure of dicyemid reproduction

The clear phylogenetic status of the enigmatic Phylum Dicyemida is still uncertain. Their primitive body plan lacks essential metazoan synapomorphies, while genetic data favor a kinship with higher lophotrochozoans. This ultrastructural study increases the confusion about this phylum by presenting an unusual gonad and sperm structure lacking all synapomorphies essential for the various phyla of the lophotrochozoans, either free-living ones or parasites. In Dicyema typus, gonadogenesis is reduced to a single somatic cell, i.e., the infusorigen's axial cell that functions as a somatic gonadal founder cell as soon as a spermatogonium takes residence in its cytoplasm. The spermiogenic cells resulting therefrom are not connected by intercellular bridges and permanently contain a bundle of microtubules in their cytoplasm, obviously a kind of "dormant" spindle having assembled without centrosomes. Primary spermatocytes develop so-called polycomplexes, multiple synaptinemal complexes. The structure of the sperm is based on a certain kind of somatic cell that has been minimally adapted to function as a sperm. The mature sperm consists in only three organelles: an ovoid nucleus with a somatic chromatin structure, numerous pore complexes and a centrally arranged cluster of coiled tubular structures; a bundle of microtubules embedded into a rim running along the nucleus longitudinal surface, projecting out of the cell like a spear; and a lipid vesicle tightly attached to one pole of the nucleus, touching there the adjacent bundle of microtubules. Immunelectron microscopy confirms the somatic condition of mature sperm, revealing somatic histone H1 immunoreactivity over the nucleus, which can be interpreted as synapomorphy shared with Protozoa, Porifera and Cnidaria. Fertilization occurs as selfing, where the sperm penetrates, "bundle of microtubules first", a primary oocyte attached vis-à-vis on the other side of the plasma membrane of the infusorigen's axial cell. This somatic situation points to an ancient evolutionary model rather than to a condition caused by retrogression due to their life as commensals.

Constrained intron structures in a microsporidian

The 2.9-Mbp genome of the microsporidian Encephalitozoon cuniculi is severely reduced and compacted, possessing only 16 known tiny spliceosomal introns. Based on motif and expression data, intron profiles were constructed to screen the genome. Twenty additional introns were predicted and verified, doubling the previous estimate. We further predict that accurate 3' splice site (3'SS) selection is accomplished via a scanning mechanism with specificity achieved by maintaining a constrained variable length between the branch point motif and 3'SS. Only introns in ribosomal protein genes exhibit positional bias, and we hypothesize that splicing could be regulating expression of these genes. The large set of new introns in non-ribosomal protein genes suggests that current models of intron loss are unlikely sufficient to explain the distribution of introns. Together, these results extend our understanding of the role of intron loss in genome evolution and contribute to a novel model for splice site selection.