Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Horizontal transmission of functionally diverse transposons is a major source of new introns

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

Transcriptomes of a fast-developing chordate uncover drastic differences in transcription factors and localized maternal RNA composition compared with those of ascidians

The larvacean Oikopleura dioica is a fast-developing chordate because of its small number of cells (∼4500 in juveniles) and rapid development to complete morphogenesis by 10 h after fertilization. Strikingly, most of its blastomeres are restricted to give rise to a single cell-type by the 32-cell stage of embryogenesis, unlike cell fate determination at the 110-cell stage in ascidians. In this study, RNA-sequencing (RNA-seq) revealed non-canonical properties of O. dioica: (1) an initial zygotic gene expression of 950 genes at the 16- to 32-cell stage; (2) 25 transcription factors (TFs) are expressed in the 32-cell stage (fewer than half of the TFs underlying gene regulatory networks in ascidian embryogenesis were lost or not expressed); (3) five maternal mRNAs localized in the vegetal-posterior blastomeres in animal and vegetal hemispheres; and (4) three maternal mRNAs localized in the small vegetal pole region of unfertilized eggs. These observations indicate that this fast-developing chordate lacks the first phase of development in ascidians: fertilization-driven ooplasmic movements that drive postplasmic RNAs toward the vegetal pole. These data have been deposited in ANISEED (https://www.aniseed.fr/) as transcriptome resources.

The complete mitogenome of an unidentified Oikopleura species

Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of Oikopleura dioica. This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.

Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles

The impact of gene loss on the diversification of taxa and the emergence of evolutionary innovations remains poorly understood. Here, our investigation on the evolution of the Fibroblast Growth Factors (FGFs) in appendicularian tunicates as a case study reveals a scenario of "less, but more" characterized by massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn underwent two bursts of duplications. Through phylogenetic analysis, synteny conservation, and gene and protein structure, we reconstruct the history of appendicularian Fgf genes, highlighting their paracrine and intracellular functions. An exhaustive analysis of developmental Fgf expression in Oikopleura dioica allows us to identify four associated evolutionary patterns characterizing the "less, but more" conceptual framework: conservation of ancestral functions; function shuffling between paralogs linked to gene losses; innovation of new functions after the duplication bursts; and function extinctions linked to gene losses. Our findings allow us to formulate novel hypotheses about the impact of Fgf losses and duplications on the transition from an ancestral ascidian-like biphasic lifestyle to the fully free-living appendicularians. These hypotheses include massive co-options of Fgfs for the development of the oikoblast and the tail fin; recruitment of Fgf11/12/13/14s into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an anterior tail FGF signaling source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis and tail absorption in appendicularians, in contrast to ascidians.

Pax3/7 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory

Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factor genes expressed during early OE patterning. Among these are two Pax3/7 copies that we named pax37A and pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 plays a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica pax37A and pax37B in the development of the OE, by using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals. We found that pax37B but not pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supported a neuroepithelial-like or a preplacodal ectoderm transcriptional signature in these cells. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features. This is supported by a fragmented gene regulatory network involved in their development that also operates in ascidian epidermal neurons.

Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa

Eleven years after the publication of the first work applying deoxyribonucleic acid (DNA) metabarcoding to zooplankton communities, the commonly known "miniCOI" barcode is widely used, becoming the marker of choice. However, several primer combinations co-exist for this barcode and a critical evaluation of their performance is needed. This article reviews the misperformance of miniCOI metabarcoding with marine zooplankton communities, comparing them to microscopy and/or other universal markers. In total, misperformances were reported for 26 zooplankton taxa, including 18 copepods and five tunicates. We report a detection failure with Class Appendicularia and contrasting performances for Oithona similis (from good correspondence to detection failure), two worldwide abundant taxa with a crucial role in the marine pelagic realm. A combination of forward primer mismatches, the presence of long poly-T inserts and a low number of reference sequences would explain the failure to detect appendicularians. However, the contrasting performance with O. similis would correspond to distinct numbers of mismatches in the forward primer in different lineages within this cryptic taxon. This is reinforced by the report of similar patterns with other locally abundant zooplankton taxa. Therefore, we strongly call for the use of miniCOI in combination with alternative methods capable of addressing these limitations.

Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians

The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories-high and low rearrangement-largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss

Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.

Tracing Homopolymers in Oikopleura dioica's Mitogenome

Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4, and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies.

Transposon-derived introns as an element shaping the structure of eukaryotic genomes

The widely accepted hypothesis postulates that the first spliceosomal introns originated from group II self-splicing introns. However, it is evident that not all spliceosomal introns in the nuclear genes of modern eukaryotes are inherited through vertical transfer of intronic sequences. Several phenomena contribute to the formation of new introns but their most common origin seems to be the insertion of transposable elements. Recent analyses have highlighted instances of mass gains of new introns from transposable elements. These events often coincide with an increase or change in the spliceosome's tolerance to splicing signals, including the acceptance of noncanonical borders. Widespread acquisitions of transposon-derived introns occur across diverse evolutionary lineages, indicating convergent processes. These events, though independent, likely require a similar set of conditions. These conditions include the presence of transposon elements with features enabling their removal at the RNA level as introns and/or the existence of a splicing mechanism capable of excising unusual sequences that would otherwise not be recognized as introns by standard splicing machinery. Herein we summarize those mechanisms across different eukaryotic lineages.

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates

Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. Using Salpingoeca rosetta as a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly in S. rosetta to its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.

Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species

Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila, or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioica suggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.

Gene networks and the evolution of olfactory organs, eyes, hair cells and motoneurons: a view encompassing lancelets, tunicates and vertebrates

Key developmental pathways and gene networks underlie the formation of sensory cell types and structures involved in chemosensation, vision and mechanosensation, and of the efferents these sensory inputs can activate. We describe similarities and differences in these pathways and gene networks in selected species of the three main chordate groups, lancelets, tunicates, and vertebrates, leading to divergent development of olfactory receptors, eyes, hair cells and motoneurons. The lack of appropriately posited expression of certain transcription factors in lancelets and tunicates prevents them from developing vertebrate-like olfactory receptors and eyes, although they generate alternative structures for chemosensation and vision. Lancelets and tunicates lack mechanosensory cells associated with the sensation of acoustic stimuli, but have gravisensitive organs and ciliated epidermal sensory cells that may (and in some cases clearly do) provide mechanosensation and thus the capacity to respond to movement relative to surrounding water. Although functionally analogous to the vertebrate vestibular apparatus and lateral line, homology is questionable due to differences in the expression of the key transcription factors Neurog and Atoh1/7, on which development of vertebrate hair cells depends. The vertebrate hair cell-bearing inner ear and lateral line thus likely represent major evolutionary advances specific to vertebrates. Motoneurons develop in vertebrates under the control of the ventral signaling molecule hedgehog/sonic hedgehog (Hh,Shh), against an opposing inhibitory effect mediated by dorsal signaling molecules. Many elements of Shh-signaling and downstream genes involved in specifying and differentiating motoneurons are also exhibited by lancelets and tunicates, but the repertoire of MNs in vertebrates is broader, indicating greater diversity in motoneuron differentiation programs.

Geography and developmental plasticity shape post-larval thermal tolerance in the golden star tunicate, Botryllus schlosseri

Local adaptation and phenotypic plasticity play key roles in mediating organisms' ability to respond to spatiotemporal variation in temperature. These two processes often act together to generate latitudinal or elevational clines in acute temperature tolerance. Phenotypic plasticity is also subject to local adaptation, with the expectation that populations inhabiting more variable environments should exhibit greater phenotypic plasticity of thermal tolerance. Here we examine the potential for local adaptation and developmental plasticity of thermal tolerance in the widespread invasive tunicate Botryllus schlosseri. By comparing five populations across a thermal gradient spanning 4.4° of latitude in the northwest Atlantic, we demonstrate that warmer populations south of the Gulf of Maine exhibit significantly increased (∼0.2 °C) post-larval temperature tolerance relative to the colder populations within it. We also show that B. schlosseri post-larvae possess a high degree of developmental plasticity for this trait, shifting their median temperature of survival (LT50) upwards by as much as 0.18 °C per 1 °C increase in environmental temperature. Lastly, we found that populations vary in their degrees of developmental plasticity, with populations that experience more pronounced short-term temperature variability exhibiting greater developmental plasticity, suggesting the local adaptation of developmental plasticity. By comparing the thermal tolerance of populations across space and through time, we demonstrate how geography and developmental plasticity have shaped thermal tolerance in B. schlosseri. These results help inform our understanding of how species are able to adjust their thermal physiology in new environments, including those encountered during invasion and under increasingly novel climate conditions.

MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes

Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.

Functional specialization of Aurora kinase homologs during oogenic meiosis in the tunicate Oikopleura dioica

A single Aurora kinase found in non-vertebrate deuterostomes is assumed to represent the ancestor of vertebrate Auroras A/B/C. However, the tunicate Oikopleura dioica, a member of the sister group to vertebrates, possesses two Aurora kinases (Aurora1 and Aurora2) that are expressed in proliferative cells and reproductive organs. Previously, we have shown that Aurora kinases relocate from organizing centers to meiotic nuclei and were enriched on centromeric regions as meiosis proceeds to metaphase I. Here, we assessed their respective functions in oogenic meiosis using dsRNA interferences. We found that Aurora1 (Aur1) was involved in meiotic spindle organization and chromosome congression, probably through the regulation of microtubule dynamics, whereas Aurora2 (Aur2) was crucial for chromosome condensation and meiotic spindle assembly. In vitro kinase assays showed that Aur1 and Aur2 had comparable levels of kinase activities. Using yeast two-hybrid library screening, we identified a few novel interaction proteins for Aur1, including c-Jun-amino-terminal kinase-interacting protein 4, cohesin loader Scc2, and mitochondrial carrier homolog 2, suggesting that Aur1 may have an altered interaction network and participate in the regulation of microtubule motors and cohesin complexes in O. dioica.

Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species

Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.

De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus

Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp, and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from nonmodel organisms in the investigation of biological phenomena.

Genome-wide identification of the opsin protein in Leptosphaeria maculans and comparison with other fungi (pathogens of Brassica napus)

The largest family of transmembrane receptors are G-protein-coupled receptors (GPCRs). These receptors respond to perceived environmental signals and infect their host plants. Family A of the GPCR includes opsin. However, there is little known about the roles of GPCRs in phytopathogenic fungi. We studied opsin in Leptosphaeria maculans, an important pathogen of oilseed rape (Brassica napus) that causes blackleg disease, and compared it with six other fungal pathogens of oilseed rape. A phylogenetic tree analysis of 31 isoforms of the opsin protein showed six major groups and six subgroups. All three opsin isoforms of L. maculans are grouped in the same clade in the phylogenetic tree. Physicochemical analysis revealed that all studied opsin proteins are stable and hydrophobic. Subcellular localization revealed that most isoforms were localized in the endoplasmic reticulum membrane except for several isoforms in Verticillium species, which were localized in the mitochondrial membrane. Most isoforms comprise two conserved domains. One conserved motif was observed across all isoforms, consisting of the BACTERIAL_OPSIN_1 domain, which has been hypothesized to have an identical sensory function. Most studied isoforms showed seven transmembrane helices, except for one isoform of V. longisporum and four isoforms of Fusarium oxysporum. Tertiary structure prediction displayed a conformational change in four isoforms of F. oxysporum that presumed differences in binding to other proteins and sensing signals, thereby resulting in various pathogenicity strategies. Protein-protein interactions and binding site analyses demonstrated a variety of numbers of ligands and pockets across all isoforms, ranging between 0 and 13 ligands and 4 and 10 pockets. According to the phylogenetic analysis in this study and considerable physiochemically and structurally differences of opsin proteins among all studied fungi hypothesized that this protein acts in the pathogenicity, growth, sporulation, and mating of these fungi differently.

Kobayashi Award 2021: Neuropeptides, receptors, and follicle development in the ascidian, Ciona intestinalis Type A: New clues to the evolution of chordate neuropeptidergic systems from biological niches

Ciona intestinalis Type A (Ciona robusta) is a cosmopolitan species belonging to the phylum Urochordata, invertebrate chordates that are phylogenetically the most closely related to the vertebrates. Therefore, this species is of interest for investigation of the evolution and comparative physiology of endocrine, neuroendocrine, and nervous systems in chordates. Our group has identified>30 Ciona neuropeptides (80% of all identified ascidian neuropeptides) primarily using peptidomic approaches combined with reference to genome sequences. These neuropeptides are classified into two groups: homologs or prototypes of vertebrate neuropeptides and novel (Ciona-specific) neuropeptides. We have also identified the cognate receptors for these peptides. In particular, we elucidated multiple receptors for Ciona-specific neuropeptides by a combination of a novel machine learning system and experimental validation of the specific interaction of the predicted neuropeptide-receptor pairs, and verified unprecedented phylogenies of receptors for neuropeptides. Moreover, several neuropeptides were found to play major roles in the regulation of ovarian follicle development. Ciona tachykinin facilitates the growth of vitellogenic follicles via up-regulation of the enzymatic activities of proteases. Ciona vasopressin stimulates oocyte maturation and ovulation via up-regulation of maturation-promoting factor- and matrix metalloproteinase-directed collagen degradation, respectively. Ciona cholecystokinin also triggers ovulation via up-regulation of receptor tyrosine kinase signaling and the subsequent activation of matrix metalloproteinase. These studies revealed that the neuropeptidergic system plays major roles in ovarian follicle growth, maturation, and ovulation in Ciona, thus paving the way for investigation of the biological roles for neuropeptides in the endocrine, neuroendocrine, nervous systems of Ciona, and studies of the evolutionary processes of various neuropeptidergic systems in chordates.

Step in Time: Conservation of Circadian Clock Genes in Animal Evolution

Over the past few decades, the molecular mechanisms responsible for circadian phenotypes of animals have been studied in increasing detail in mammals, some insects, and other invertebrates. Particular circadian proteins and their interactions are shared across evolutionary distant animals, resulting in a hypothesis for the canonical circadian clock of animals. As the number of species for which the circadian clockwork has been described increases, the circadian clock in animals driving cyclical phenotypes becomes less similar. Our focus in this review is to develop and synthesize the current literature to better understand the antiquity and evolution of the animal circadian clockwork. Here, we provide an updated understanding of circadian clock evolution in animals, largely through the lens of conserved genes characterized in the circadian clock identified in bilaterian species. These comparisons reveal extensive variation within the likely composition of the core clock mechanism, including losses of many genes, and that the ancestral clock of animals does not equate to the bilaterian clock. Despite the loss of these core genes, these species retain circadian behaviors and physiology, suggesting novel clocks have evolved repeatedly. Additionally, we highlight highly conserved cellular processes (e.g., cell division, nutrition) that intersect with the circadian clock of some animals. The conservation of these processes throughout the animal tree remains essentially unknown, but understanding their role in the evolution and maintenance of the circadian clock will provide important areas for future study.

Laboratory study of Fritillaria lifecycle reveals key morphogenetic events leading to genus-specific anatomy

A fascinating variety of adult body plans can be found in the Tunicates, the closest existing relatives of vertebrates. A distinctive feature of the larvacean class of pelagic tunicates is the presence of a highly specialized surface epithelium that produces a cellulose test, the “larvacean house”. While substantial differences exist between the anatomy of larvacean families, most of the ontogeny is derived from the observations of a single genus, Oikopleura. We present the first study of Fritillaria development based on the observation of individuals reproduced in the laboratory. Like the other small epipelagic species Oikopleura dioica, the larvae of Fritillaria borealis grow rapidly in the laboratory, and they acquire the adult form within a day. We could show that major morphological differences exhibited by Fritillaria and Oikopleura adults originate from a key developmental stage during larval organogenesis. Here, the surface epithelium progressively retracts from the posterior digestive organs of Fritillaria larvae, and it establishes house-producing territories around the pharynx. Our results show that the divergence between larvacean genera was associated with a profound rearrangement of the mechanisms controlling the differentiation of the larval ectoderm.

Integrative omics approaches for biosynthetic pathway discovery in plants

Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.

Intron size minimisation in teleosts

Background

Spliceosomal introns are parts of primary transcripts that are removed by RNA splicing. Although introns apparently do not contribute to the function of the mature transcript, in vertebrates they comprise the majority of the transcribed region increasing the metabolic cost of transcription. The persistence of long introns across evolutionary time suggests functional roles that can offset this metabolic cost. The teleosts comprise one of the largest vertebrate clades. They have unusually compact and variable genome sizes and provide a suitable system for analysing intron evolution.

Results

We have analysed intron lengths in 172 vertebrate genomes and show that teleost intron lengths are relatively short, highly variable and bimodally distributed. Introns that were long in teleosts were also found to be long in mammals and were more likely to be found in regulatory genes and to contain conserved sequences. Our results argue that intron length has decreased in parallel in a non-random manner throughout teleost evolution and represent a deviation from the ancestral state.

Conclusion

Our observations indicate an accelerated rate of intron size evolution in the teleosts and that teleost introns can be divided into two classes by their length. Teleost intron sizes have evolved primarily as a side-effect of genome size evolution and small genomes are dominated by short introns (<256 base pairs). However, a non-random subset of introns has resisted this process across the teleosts and these are more likely have functional roles in all vertebrate clades.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-022-08760-w).

Neighbours matter: Effects of genomic organization on gene expression plasticity in response to environmental stresses during biological invasions

Gene expression regulation has been widely recognized as an important molecular mechanism underlying phenotypic plasticity in environmental adaptation. However, it remains largely unexplored on the effects of genomic organization on gene expression plasticity under environmental stresses during biological invasions. Here, we use an invasive model ascidian, Ciona robusta, to investigate how genomic organization affects gene expression in response to salinity stresses during range expansions. Our study showed that neighboring genes were co-expressed and approximately 30% of stress responsive genes were physically clustered on chromosomes. Such coordinated expression was substantially affected by the physical distance and orientation of genes. Interestingly, the overall expression correlation of neighboring genes was significantly decreased under high salinity stresses, illustrating that the co-expression regulation could be disrupted by salinity challenges. Furthermore, the clustering of genes was associated with their function constraints and expression patterns - operon genes enriched in gene expression machinery had the highest transcriptional activity and expression stability. Notably, our analyses showed that the tail-to-tail genes, mainly involved in biological functions related to phosphorylation, homeostatic process, and ion transport, exhibited higher intrinsic expression variability and greater response to salinity challenges. Altogether, the results obtained here provide new insights into the effects of gene organization on gene expression plasticity under environmental challenges, hence improving our knowledge on mechanisms of rapid environmental adaptation during biological invasions.

Firefly genomes illuminate the evolution of beetle bioluminescent systems

Fireflies are one of the best-known bioluminescent organisms, and the reaction mechanism and ecological utility of bioluminescence have been well-studied. Genome assemblies of six species of bioluminescent beetles have recently been published. These studies have focused on the evolution of novelties; luciferase, and the biosynthesis of luciferin and defensive chemicals. For example, clustering of the luciferase gene with acyl-CoA synthetase genes on a chromosome in luminous beetle genomes suggests the involvement of tandem gene duplications and neofunctionalization during the evolution of beetle bioluminescence. Several candidate genes for critical roles in beetle bioluminescence have been identified, but their functional analyses are still ongoing. The establishment of a long-term mass-rearing system and strain will be the key for the post-genome research on bioluminescent beetles. Lastly, the application of contemporary chromosome-scale genome assembly techniques to luminous beetles will help resolve outstanding evolutionary questions, such as how many times bioluminescence evolved in this clade.

Evolutionary History of TOPIIA Topoisomerases in Animals

TOPIIA topoisomerases are required for the regulation of DNA topology by DNA cleavage and re-ligation and are important targets of antibiotic and anticancer agents. Humans possess two TOPIIA paralogue genes (TOP2A and TOP2B) with high sequence and structural similarity but distinct cellular functions. Despite their functional and clinical relevance, the evolutionary history of TOPIIA is still poorly understood. Here we show that TOPIIA is highly conserved in Metazoa. We also found that TOPIIA paralogues from jawed and jawless vertebrates had different origins related with tetraploidization events. After duplication, TOP2B evolved under a stronger purifying selection than TOP2A, perhaps promoted by the more specialized role of TOP2B in postmitotic cells. We also detected genetic signatures of positive selection in the highly variable C-terminal domain (CTD), possibly associated with adaptation to cellular interactions. By comparing TOPIIA from modern and archaic humans, we found two amino acid substitutions in the TOP2A CTD, suggesting that TOP2A may have contributed to the evolution of present-day humans, as proposed for other cell cycle-related genes. Finally, we identified six residues conferring resistance to chemotherapy differing between TOP2A and TOP2B. These six residues could be targets for the development of TOP2A-specific inhibitors that would avoid the side effects caused by inhibiting TOP2B. Altogether, our findings clarify the origin, diversification and selection pressures governing the evolution of animal TOPIIA.

Omics Studies for the Identification of Ascidian Peptides, Cognate Receptors, and Their Relevant Roles in Ovarian Follicular Development

Omics studies contribute to the elucidation of genomes and profiles of gene expression. In the ascidian Ciona intestinalis Type A (Ciona robusta), mass spectrometry (MS)-based peptidomic studies have detected numerous Ciona-specific (nonhomologous) neuropeptides as well as Ciona homologs of typical vertebrate neuropeptides and hypothalamic peptide hormones. Candidates for cognate G protein-coupled receptors (GPCRs) for these peptides have been found in the Ciona transcriptome by two ways. First, Ciona homologous GPCRs of vertebrate counterparts have been detected by sequence homology searches of cognate transcriptomes. Second, the transcriptome-derived GPCR candidates have been used for machine learning-based systematic prediction of interactions not only between Ciona homologous peptides and GPCRs but also between novel Ciona peptides and GPCRs. These data have ultimately led to experimental evidence for various Ciona peptide-GPCR interactions. Comparative transcriptomics between the wildtype and Ciona vasopressin (CiVP) gene-edited Ciona provide clues to the biological functions of CiVP in ovarian follicular development and whole body growth. Furthermore, the transcriptomes of follicles treated with peptides, such as Ciona tachykinin and cionin (a Ciona cholecystokinin homolog), have revealed key regulatory genes for Ciona follicle growth, maturation, and ovulation, eventually leading to the verification of essential and novel molecular mechanisms underlying these biological events. These findings indicate that omics studies, combined with artificial intelligence and single-cell technologies, pave the way for investigating in greater details the nervous, neuroendocrine, and endocrine systems of ascidians and the molecular and functional evolution and diversity of peptidergic regulatory networks throughout chordates.

Developmental biology of the larvacean Oikopleura dioica: Genome resources, functional screening, and imaging

The larvacean Oikopleura dioica is a cosmopolitan planktonic chordate and is closely related to vertebrates. It is characterized by a tadpole-shaped morphology with notochord flanked by muscle in the tail and brain on the dorsal side, a short life cycle of five days, a compact genome of approximately 56 Mb, a simple and transparent body with a small number of cells (~4000 in functional juveniles), invariant embryonic cell lineages, and fast development that ensures complete morphogenesis and organ formation 10 h after fertilization. With these features, this marine chordate is a promising and advantageous animal model in which genetic manipulation is feasible. In this review, we introduce relevant resources and modern techniques that have been developed: (1) Genome and transcriptomes. Oikopleura dioica has the smallest genome among non-parasitic metazoans. Its genome databases have been generated using three geographically distant O. dioica populations, and several intra-species sequence differences are becoming evident; (2) Functional genetic knockdown techniques. Comprehensive screening of genes is feasible using ovarian microinjection and double-strand DNA-induced gene knockdown; and (3) Live imaging of embryos and larvae. Application of these techniques has uncovered novel aspects of development, including meiotic cell arrest, left-right patterning, epidermal cell patterning, and mouth formation involving the connection of ectoderm and endoderm sheets. Oikopleura dioca has become very useful for developmental and evolutionary studies in chordates.

The Genome of the "Sea Vomit" Didemnum vexillum

Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as "sea vomit", is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the "sea vomit" genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.

The evolution of the metazoan Toll receptor family and its expression during protostome development

BACKGROUND

Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa.

RESULTS

We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development.

CONCLUSIONS

Our findings suggest that a clade α TLR gene (TLR-Ca) and a clade β/γ TLR gene (TLR-Cβ/γ) were already present in the cnidarian-bilaterian common ancestor. However, although TLR-Ca was conserved in cnidarians, TLR-Cβ/γ was lost during the early evolution of these taxa. Moreover, TLR-Cβ/γ duplicated to generate TLR-Cβ and TLR-Cγ in the lineage to the last common protostome-deuterostome ancestor. TLR-Ca, TLR-Cβ and TLR-Cγ further expanded generating the three major TLR clades. While all three clades radiated in several spiralian lineages, specific TLRs clades have been presumably lost in other lineages. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests a likely role in development.

Germline development during embryogenesis of the larvacean, Oikopleura dioica

Germ cells develop into eggs and sperms and represent a lineage that survives through multiple generations. Germ cell specification during embryogenesis proceeds through one of two basic modes: either the cell-autonomous mode or the inductive mode. In the cell-autonomous mode, specification of germ cell fate involves asymmetric partitioning of the specialized maternal cytoplasm, known as the germplasm. Oikopleura dioica is a larvacean (class Appendicularia) and a chordate. It is regarded as a promising animal model for studying chordate development because of its short life cycle (5 days) and small genome size (∼60 ​Mb). We show that their embryos possess germplasm, as observed in ascidians (class Ascidiacea). The vegetal cytoplasm shifted towards the future posterior pole before the first cleavage occurred. A bilateral pair of primordial germ cells (PGC, B11 ​cells) was formed at the posterior pole at the 32-cell stage through two rounds of unequal cleavage. These B11 ​cells did not undergo further division before hatching of the tadpole-shaped larvae. The centrosome-attracting body (CAB) is a subcellular structure that contains the germplasm and plays crucial roles in germ cell development in ascidians. The presence of CAB with germplasm was observed in the germline lineage cells of larvaceans via electron microscopy and using extracted embryos. The CAB appeared at the 8-cell stage and persisted until the middle stage of embryogenesis. The antigen for the phosphorylated histone 3 antibody was localized to the CAB and persisted in the PGC until hatching after the CAB disappeared. Maternal snail mRNA, which encodes a transcription factor, was co-localized with the antigen for the H3S28p antibody. Furthermore, we found a novel PGC-specific subcellular structure that we call the germ body (GB). This study thus highlights the conserved and non-conserved features of germline development between ascidians and larvaceans. The rapid development and short life cycle (five days) of O. dioica would open the way to genetically analyze germ cell development in the future.

Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species

Spliceosomal introns are pervasive in eukaryotes. Intron gains and losses have occurred throughout evolution, but the origin of new introns is unclear. Stwintrons are complex intervening sequences where one of the sequence elements (5′-donor, lariat branch point element or 3′-acceptor) necessary for excision of a U2 intron (external intron) is itself interrupted by a second (internal) U2 intron. In Hypoxylaceae, a family of endophytic fungi, we uncovered scores of donor-disrupted stwintrons with striking sequence similarity among themselves and also with canonical introns. Intron–exon structure comparisons suggest that these stwintrons have proliferated within diverging taxa but also give rise to proliferating canonical introns in some genomes. The proliferated (stw)introns have integrated seamlessly at novel gene positions. The recently proliferated (stw)introns appear to originate from a conserved ancestral stwintron characterised by terminal inverted repeats (45–55 nucleotides), a highly symmetrical structure that may allow the formation of a double-stranded intron RNA molecule. No short tandem duplications flank the putatively inserted intervening sequences, which excludes a DNA transposition-based mechanism of proliferation. It is tempting to suggest that this highly symmetrical structure may have a role in intron proliferation by (an)other mechanism(s).

ExOrthist: a tool to infer exon orthologies at any evolutionary distance

Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).

Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins

Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metallothionein (MT) proteins in O. dioica. MTs are a heterogeneous group of modular proteins defined by their cysteine (C)-rich domains, which confer the capacity of coordinating different transition metal ions. O. dioica has two MTs, a bi-modular OdiMT1 consisting of two domains (t-12C and 12C), and a multi-modular OdiMT2 with six t-12C/12C repeats. By means of mass spectrometry and spectroscopy of metal-protein complexes, we have shown that the 12C domain is able to autonomously bind four divalent metal ions, although the t-12C/12C pair –as it is found in OdiMT1– is the optimized unit for divalent metal binding. We have also shown a direct relationship between the number of the t-12C/12C repeats and the metal-binding capacity of the MTs, which means a stepwise mode of functional and structural evolution for OdiMT2. Finally, after analyzing four different O. dioica populations worldwide distributed, we have detected several OdiMT2 variants with changes in their number of t-12C/12C domain repeats. This finding reveals that the number of repeats fluctuates between current O. dioica populations, which provides a new perspective on the evolution of domain repeat proteins.

Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

Nkx2-1 and FoxE regionalize glandular (mucus-producing) and thyroid-equivalent traits in the endostyle of the chordate Oikopleura dioica

The endostyle is a ventral pharyngeal organ used for internal filter feeding of basal chordates and is considered homologous to the follicular thyroid of vertebrates. It contains mucus-producing (glandular) and thyroid-equivalent regions organized along the dorsoventral (DV) axis. Although thyroid-related genes (Nkx2-1, FoxE, and thyroid peroxidase (TPO)) are known to be expressed in the endostyle, their roles in establishing regionalization within the organ have not been demonstrated. We report that Nkx2-1 and FoxE are essential for establishing DV axial identity in the endostyle of Oikopleura dioica. Genome and expression analyses showed von Willebrand factor-like (vWFL) and TPO/dual oxidase (Duox)/Nkx2-1/FoxE as orthologs of glandular and thyroid-related genes, respectively. Knockdown experiments showed that Nkx2-1 is necessary for the expression of glandular and thyroid-related genes, whereas FoxE is necessary only for thyroid-related genes. Moreover, Nkx2-1 expression is necessary for FoxE expression in larvae during organogenesis. The results demonstrate the essential roles of Nkx2-1 and FoxE in establishing regionalization in the endostyle, including (1) the Nkx2-1-dependent glandular region, and (2) the Nkx2-1/FoxE-dependent thyroid-equivalent region. DV axial regionalization may be responsible for organizing glandular and thyroid-equivalent traits of the pharynx along the DV axis.

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

Background

The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65–70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved.

Results

Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome.

Conclusions

We show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly of O. dioica’s highly polymorphic genome. This genome assembly opens up the possibility of cross-genome comparison between O. dioica populations, as well as of studies of chromosomal evolution in this lineage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07512-6.

Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species

Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.

SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

BACKGROUND

Spliced leader (SL) trans-splicing replaces the 5' end of pre-mRNAs with the spliced leader, an exon derived from a specialised non-coding RNA originating from elsewhere in the genome. This process is essential for resolving polycistronic pre-mRNAs produced by eukaryotic operons into monocistronic transcripts. SL trans-splicing and operons may have independently evolved multiple times throughout Eukarya, yet our understanding of these phenomena is limited to only a few well-characterised organisms, most notably C. elegans and trypanosomes. The primary barrier to systematic discovery and characterisation of SL trans-splicing and operons is the lack of computational tools for exploiting the surge of transcriptomic and genomic resources for a wide range of eukaryotes.

RESULTS

Here we present two novel pipelines that automate the discovery of SLs and the prediction of operons in eukaryotic genomes from RNA-Seq data. SLIDR assembles putative SLs from 5' read tails present after read alignment to a reference genome or transcriptome, which are then verified by interrogating corresponding SL RNA genes for sequence motifs expected in bona fide SL RNA molecules. SLOPPR identifies RNA-Seq reads that contain a given 5' SL sequence, quantifies genome-wide SL trans-splicing events and predicts operons via distinct patterns of SL trans-splicing events across adjacent genes. We tested both pipelines with organisms known to carry out SL trans-splicing and organise their genes into operons, and demonstrate that (1) SLIDR correctly detects expected SLs and often discovers novel SL variants; (2) SLOPPR correctly identifies functionally specialised SLs, correctly predicts known operons and detects plausible novel operons.

CONCLUSIONS

SLIDR and SLOPPR are flexible tools that will accelerate research into the evolutionary dynamics of SL trans-splicing and operons throughout Eukarya and improve gene discovery and annotation for a wide range of eukaryotic genomes. Both pipelines are implemented in Bash and R and are built upon readily available software commonly installed on most bioinformatics servers. Biological insight can be gleaned even from sparse, low-coverage datasets, implying that an untapped wealth of information can be retrieved from existing RNA-Seq datasets as well as from novel full-isoform sequencing protocols as they become more widely available.

A cis-regulatory change underlying the motor neuron-specific loss of Ebf expression in immotile tunicate larvae

Many species in the tunicate family Molgulidae have independently lost their swimming larval form and instead develop as tailless, immotile larvae. These larvae do not develop structures that are essential for swimming such as the notochord, otolith, and tail muscles. However, little is known about neural development in these nonswimming larvae. Here, we studied the patterning of the Motor Ganglion (MG) of Molgula occulta, a nonswimming species. We found that spatial patterns of MG neuron regulators in this species are conserved, compared with species with swimming larvae, suggesting that the gene networks regulating their expression are intact despite the loss of swimming. However, expression of the key motor neuron regulatory gene Ebf (Collier/Olf/EBF) was reduced in the developing MG of M. occulta when compared with molgulid species with swimming larvae. This was corroborated by measuring allele-specific expression of Ebf in hybrid embryos from crosses of M. occulta with the swimming species M. oculata. Heterologous reporter construct assays in the model tunicate species Ciona robusta revealed a specific cis-regulatory sequence change that reduces expression of Ebf in the MG, but not in other cells. Taken together, these data suggest that MG neurons are still specified in M. occulta larvae, but their differentiation might be impaired due to reduction of Ebf expression levels.

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

BACKGROUND

Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization.

RESULTS

We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions.

CONCLUSION

These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.

Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family

Collagen triple helix repeat containing protein 1 (Cthrc1) is a secreted glycoprotein reported to regulate collagen deposition and to be linked to the Transforming growth factor β/Bone morphogenetic protein and the Wnt/planar cell polarity pathways. It was first identified as being induced upon injury to rat arteries and was found to be highly expressed in multiple human cancer types. Here, we explore the phylogenetic and evolutionary trends of this metazoan gene family, previously studied only in vertebrates. We identify Cthrc1 orthologs in two distant cnidarian species, the sea anemone Nematostella vectensis and the hydrozoan Clytia hemisphaerica, both of which harbor multiple copies of this gene. We find that Cthrc1 clade-specific diversification occurred multiple times in cnidarians as well as in most metazoan clades where we detected this gene. Many other groups, such as arthropods and nematodes, have entirely lost this gene family. Most vertebrates display a single highly conserved gene, and we show that the sequence evolutionary rate of Cthrc1 drastically decreased within the gnathostome lineage. Interestingly, this reduction coincided with the origin of its conserved upstream neighboring gene, Frizzled 6 (FZD6), which in mice has been shown to functionally interact with Cthrc1. Structural modeling methods further reveal that the yet uncharacterized C-terminal domain of Cthrc1 is similar in structure to the globular C1q superfamily domain, also found in the C-termini of collagens VIII and X. Thus, our studies show that the Cthrc1 genes are a collagen-like family with a variable short collagen triple helix domain and a highly conserved C-terminal domain structure resembling the C1q family.

Conservative route to genome compaction in a miniature annelid

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.

This study reports the genome of the miniature segmented annelid Dimorphilus gyrociliatus and reveals no drastic changes in genome architecture and regulation, unlike other cases of genome miniaturization.

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt, Styela clava, is an important invasive species. We used the chromosomal-level genome and transcriptome of S. clava to explore its genomic- and molecular-network-based mechanisms of adaptation to environments. Compared with Ciona intestinalis type A (C. robusta), the size of the S. clava genome was expanded by 2-fold, although the gene number was comparable. An increase in transposon number and variation in dominant types were identified as potential expansion mechanisms. In the S. clava genome, the number of genes encoding the heat-shock protein 70 family and members of the complement system was expanded significantly, and cold-shock protein genes were transferred horizontally into the S. clava genome from bacteria. The expanded gene families potentially play roles in the adaptation of S. clava to its environments. The loss of key genes in the galactan synthesis pathway might explain the distinct tunic structure and hardness compared with the ascidian Ciona species. We demonstrated further that the integrated thyroid hormone pathway participated in the regulation of larval metamorphosis that provides S. clava with two opportunities for adapting to their environment. Thus, our report of the chromosomal-level leathery sea squirt genome provides a comprehensive genomic basis for the understanding of environmental adaptation in tunicates.

Mouth opening is mediated by separation of dorsal and ventral daughter cells of the lip precursor cells in the larvacean, Oikopleura dioica

Mouth formation involves the processes of mouth opening, formation of the oral cavity, and the development of associated sensory organs. In deuterostomes, the surface ectoderm and the anterior part of the archenteron are reconfigured and reconnected to make a mouth opening. This study of the larval development of the larvacean, Oikopleura dioica, investigates the cellular organization of the oral region, the developmental processes of the mouth, and the formation of associated sensory cells. O. dioica is a simple chordate whose larvae are transparent and have a small number of constituent cells. It completes organ morphogenesis in 7 h, between hatching 3 h after fertilization and the juvenile stage at 10 h, when it attains adult form and starts to feed. It has two types of mechanosensory cell embedded in the oral epithelium, which is a single layer of cells. There are twenty coronal sensory cells in the circumoral nerve ring and two dorsal sensory organ cells. Two bilateral lip precursor cells (LPCs), facing the anterior surface, divide dorsoventrally and make a wedge-shaped cleft between the two daughter cells named the dorsal lip cell (DLC) and the ventral lip cell (VLC). Eventually, the DLC and VLC become detached and separated into dorsal and ventral lips, triggering mouth opening. This is an intriguing example of cell division itself contributing to morphogenesis. The boundary between the ectoderm and endoderm is present between the lip cells and coronal sensory cells. All oral sensory cells, including dorsal sensory organ cells, were of endodermal origin and were not derived from the ectodermal placode. These observations on mouth formation provide a cellular basis for further studies at a molecular level, in this simple chordate.

A genome database for a Japanese population of the larvacean Oikopleura dioica

The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.