Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle

Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation

Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Phosphorus (P) is a limiting macronutrient for dinoflagellate growth in the ocean. Previous studies have been focused on the physiological response of dinoflagellates to ambient P changes. However, the whole-genome's molecular mechanisms are poorly understood. In this study, RNA-Seq was utilized to compare the global gene expression patterns of a marine diarrheic shellfish poisoning (DSP) toxin-producing dinoflagellate, Prorocentrum lima, grown in inorganic P-replete and P-deficient conditions. A total of 148 unigenes were significantly up-regulated, and 30 unigenes were down-regulated under 1/4 P-limited conditions, while 2708 unigenes were significantly up-regulated, and 284 unigenes were down-regulated under 1/16 P-limited conditions. KEGG enrichment analysis of the differentially expressed genes shows that genes related to ribosomal proteins, glycolysis, fatty acid biosynthesis, phagosome formation, and ubiquitin-mediated proteolysis are found to be up-regulated, while most of the genes related to photosynthesis are down-regulated. Further analysis shows that genes encoding P transporters, organic P utilization, and endocytosis are significantly up-regulated in the P-limited cells, indicating a strong ability of P. lima to utilize dissolved inorganic P as well as intracellular organic P. These transcriptomic data are further corroborated by biochemical and physiological analyses, which reveals that under P deficiency, cellular contents of starch, lipid, and toxin increase, while photosynthetic efficiency declines. Our results indicate that has P. lima evolved diverse strategies to acclimatize to low P environments. The accumulation of carbon sources and DSP toxins could provide protection for P. lima to cope with adverse environmental conditions.

Bacterial origin of a key innovation in the evolution of the vertebrate eye

The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that acquisition of bacterial genes has had on vertebrate evolution.

Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

Background

Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference.

Results

More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants.

Conclusions

Our work provides explanation for “amphioxus polymorphism paradox” in a micro view, and generates an enhanced genomic dataset for amphioxus research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01038-w.

The invertebrate chordate amphioxus gives clues to vertebrate origins

Amphioxus (cepholochordates) have long been used to infer how the vertebrates evolved from their invertebrate ancestors. However, some of the body part homologies between amphioxus and vertebrates have been controversial. This is not surprising as the amphioxus and vertebrate lineages separated half a billion years ago-plenty of time for independent loss and independent gain of features. The development of new techniques in the late 20th and early 21st centuries including transmission electron microscopy and serial blockface scanning electron microscopy in combination with in situ hybridization and immunocytochemistry to reveal spatio-temporal patterns of gene expression and gene products have greatly strengthened inference of some homologies (like those between regions of the central nervous system), although others (like nephridia) still need further support. These major advances in establishing homologies between amphioxus and vertebrates, together with strong support from comparative genomics, have firmly established amphioxus as a stand-in or model for the ancestral vertebrate.

Laboratory Culture and Mutagenesis of Amphioxus (Branchiostoma floridae)

Cephalochordates (amphioxus) are invertebrate chordates closely related to vertebrates. As they are evolving very slowly, they are proving to be very appropriate for developmental genetics studies aimed at understanding how vertebrates evolved from their invertebrate ancestors. To date, techniques for gene knockdown and overexpression have been developed, but methods for continuous breeding cultures and generating germline mutants have been developed only recently. Here we describe methods for continuous laboratory breeding cultures of the cephalochordate Branchiostoma floridae and the TALEN and Tol2 methods for mutagenesis. Included are strategies for analyzing the mutants and raising successive generations to obtain homozygotes. These methods should be applicable to any warm water species of cephalochordates with a relatively short generation time of 3-4 months and a life span of 3 years or more.

Cephalochordates: A window into vertebrate origins

How vertebrates evolved from their invertebrate ancestors has long been a central topic of discussion in biology. Evolutionary developmental biology (evodevo) has provided a new tool-using gene expression patterns as phenotypic characters to infer homologies between body parts in distantly related organisms-to address this question. Combined with micro-anatomy and genomics, evodevo has provided convincing evidence that vertebrates evolved from an ancestral invertebrate chordate, in many respects resembling a modern amphioxus. The present review focuses on the role of evodevo in addressing two major questions of chordate evolution: (1) how the vertebrate brain evolved from the much simpler central nervous system (CNS) in of this ancestral chordate and (2) whether or not the head mesoderm of this ancestor was segmented.

Molecular Fingerprint of Amphioxus Frontal Eye Illuminates the Evolution of Homologous Cell Types in the Chordate Retina

The evolution of the vertebrate eye remains so far unresolved. Amphioxus frontal eye pigment cells and photoreceptors were proposed to be homologous to vertebrate photoreceptors and retinal pigmented epithelium, based on ultrastructural morphology and gene expression analysis in B. floridae. Here, we present comparative molecular data using two additional amphioxus species, a closely related B. lanceolatum, and the most divergent A. lucayanum. Taking advantage of a unique set of specific antibodies we characterized photoreceptors and putative interneurons of the frontal eye and investigated its neuronal circuitry. Our results corroborate generally conserved molecular fingerprint among cephalochordate species. Furthermore, we performed pharmacological perturbations and found that the Notch signaling pathway, a key regulator of retina development in vertebrates, is required for correct ratios among frontal eye cell types. In summary, our study provides a valuable insight into cell-type relationships in chordate visual organs and strengthens the previously proposed homology between amphioxus frontal eye and vertebrate eyes.

Whole-Genome Resequencing of Twenty Branchiostoma belcheri Individuals Provides a Brand-New Variant Dataset for Branchiostoma

As the extant representatives of the basal chordate lineage, amphioxi (including the genera Branchiostoma, Asymmetron and Epigonichthys) play important roles in tracing the state of chordate ancestry. Previous studies have reported that members of the Branchiostoma species have similar morphological phenotypic characteristics, but in contrast, there are high levels of genetic polymorphisms in the populations. Here, we resequenced 20 Branchiostomabelcheri genomes to an average depth of approximately 12.5X using the Illumina HiSeq 2000 platform. In this study, over 52 million variations (~12% of the total genome) were detected in the B. belcheri population, and an average of 12.8 million variations (~3% of the total genome) were detected in each individual, confirming that Branchiostoma is one of the most genetically diverse species sequenced to date. Demographic inference analysis highlighted the role of historical global temperature in the long-term population dynamics of Branchiostoma, and revealed a population expansion at the Greenlandian stage of the current geological epoch. We detected 594 Single nucleotide polymorphism and 148 Indels in the Branchiostoma mitochondrial genome, and further analyzed their genetic mutations. A recent study found that the epithelial cells of the digestive tract in Branchiostoma can directly phagocytize food particles and convert them into absorbable nontoxic nutrients using powerful digestive and immune gene groups. In this study, we predicted all potential mutations in intracellular digestion-associated genes. The results showed that most “probably damaging” mutations were related to rare variants (MAF<0.05) involved in strengthening or weakening the intracellular digestive capacity of Branchiostoma. Due to the extremely high number of polymorphisms in the Branchiostoma genome, our analysis with a depth of approximately 12.5X can only be considered a preliminary analysis. However, the novel variant dataset provided here is a valuable resource for further investigation of phagocytic intracellular digestion in Branchiostoma and determination of the phenotypic and genotypic features of Branchiostoma.

Lampreys, the jawless vertebrates, contain three Pax6 genes with distinct expression in eye, brain and pancreas

The transcription factor Pax6 is crucial for the development of the central nervous system, eye, olfactory system and pancreas, and is implicated in human disease. While a single Pax6 gene exists in human and chicken, Pax6 occurs as a gene family in other vertebrates, with two members in elephant shark, Xenopus tropicalis and Anolis lizard and three members in teleost fish such as stickleback and medaka. However, the complement of Pax6 genes in jawless vertebrates (cyclostomes), the sister group of jawed vertebrates (gnathostomes), is unknown. Using a combination of BAC sequencing and genome analysis, we discovered three Pax6 genes in lampreys. Unlike the paired-less Pax6 present in some gnathostomes, all three lamprey Pax6 have a highly conserved full-length paired domain. All three Pax6 genes are expressed in the eye and brain, with variable expression in other tissues. Notably, lamprey Pax6α transcripts are found in the pancreas, a vertebrate-specific organ, indicating the involvement of Pax6 in development of the pancreas in the vertebrate ancestor. Multi-species sequence comparisons revealed only a single conserved non-coding element, in the lamprey Pax6β locus, with similarity to the PAX6 neuroretina enhancer. Using a transgenic zebrafish enhancer assay we demonstrate functional conservation of this element over 500 million years of vertebrate evolution.

Phagocytic intracellular digestion in amphioxus (Branchiostoma)

The digestive methods employed by amphioxus (Branchiostoma)—both intracellular phagocytic digestion and extracellular digestion—have been discussed since 1937. Recent studies also show that epithelial cells lining the Branchiostoma digestive tract can express many immune genes. Here, in Branchiostoma belcheri, using a special tissue fixation method, we show that some epithelial cells, especially those lining the large diverticulum protruding from the gut tube, phagocytize food particles directly, and Branchiostoma can rely on this kind of phagocytic intracellular digestion to obtain energy throughout all stages of its life. Gene expression profiles suggest that diverticulum epithelial cells have functional features of both digestive cells and phagocytes. In starved Branchiostoma, these cells accumulate endogenous digestive and hydrolytic enzymes, whereas, when sated, they express many kinds of immune genes in response to stimulation by phagocytized food particles. We also found that the distal hindgut epithelium can phagocytize food particles, but not as many. These results illustrate phagocytic intercellular digestion in Branchiostoma, explain why Branchiostoma digestive tract epithelial cells express typical immune genes and suggest that the main physiological function of the Branchiostoma diverticulum is different from that of the vertebrate liver.

The Natural History of Teneurins: A Billion Years of Evolution in Three Key Steps

The entire evolutionary history of the animal gene family, Teneurin, can be summed up in three key steps, plus three salient footnotes. In a shared ancestor of all bilaterians, the first step began with gene fusions that created a protein with an amino-terminal intracellular domain bridged via a single transmembrane helix to extracellular EGF-like domains. This first step was completed with a further gene fusion: an additional carboxy-terminal stretch of about 2000 amino acids (aa) was adopted, as-a-whole, from bacteria. The 2000 aa structure in Teneurin was recently solved in three dimensions. The 2000 aa region appears in a number of bacteria, yet was co-opted solely into Teneurin, and into no other eukaryotic proteins. Outside of bilaterian animals, no Teneurins exist, with a “Monosiga brevicollis caveat” brought below, as ‘the third footnote.” Subsequent to the “urTeneurin’s” genesis-by-fusions, all bilaterians bore a single Teneurin gene, always encoding an extraordinarily conserved Type II transmembrane protein with invariant domain content and order. The second key step was a duplication that led to an exception to singleton Teneurin genomes. A pair of Teneurin paralogs, Ten-a and Ten-m, are found in representatives of all four Arthropod sub-phyla, in: insects, crustaceans, myriapods, and chelicerates. In contrast, in every other protostome species’ genome, including those of all non-Arthropod ecdysozoan phyla, only a single Teneurin gene occurs. The closest, sister, phylum of arthropods, the Onychophorans (velvet worms), bear a singleton Teneurin. Ten-a and Ten-m therefore arose from a duplication in an urArthropod only after Arthropods split from Onychophorans, but before the splits that led to the four Arthropod sub-phyla. The third key step was a quadruplication of Teneurins at the root of vertebrate radiation. Four Teneurin paralogs (Teneurins 1 through 4) arose first by a duplication of a single chordate gene likely leading to one 1/4–type gene, and one 2/3-type gene: the two copies found in extant jawless vertebrates. Relatively soon thereafter, a second duplication round yielded the -1, -2, -3, and -4 paralog types now found in all jawed vertebrates, from sharks to humans. It is possible to assert that these duplication events correlate well to the Ohno hypothesized 2R (two round) vertebrate whole genome duplication (WGD), as refined in more recent treatments. The quadruplication can therefore be placed at approximately 400 Myr ago. Echinoderms, hemichordates, cephalochordates, and urochordates have only a single copy of Teneurin in their genomes. These deuterostomes and non-vertebrate chordates provide the anchor showing that the quadruplication happened at the root of vertebrates. A first footnote must be brought concerning some of the ‘invertebrate’ relatives of vertebrates, among Deuterostomes. A family of genes that encode 7000 aa proteins was derived from, but is distinct from, the Teneurin family. This distinct family arose early in deuterostomes, yet persists today only in hemichordate and cephalochordate genomes. They are named here TRIPs (Teneurin-related immense proteins). As a second of three ‘footnotes’: a limited number of species exist with additional Teneurin gene copies. However, these further duplications of Teneurins occur for paralog types (a, m, or 1–4) only in specific lineages within Arthropods or Vertebrates. All examples are paralog duplications that evidently arose in association with lineage specific WGDs. The increased Teneurin paralog numbers correlate with WGDs known and published in bony fish, Xenopus, plus select Chelicerates lineages and Crustaceans. The third footnote, alluded to above, is that a Teneurin occurs in one unicellular species: Monosiga brevicollis. Teneurins are solely a metazoan, bilaterian-specific family, to the exclusion of the Kingdoms of prokaryotes, plants, fungi, and protists. The single exception occurs among the unicellular, opisthokont, closest relatives of metazoans, the choanoflagellates. There is a Teneurin in Monosiga brevicollis, one species of the two fully sequenced choanoflagellate species. In contrast, outside of triploblast-bilaterians, there are no Teneurins in any diploblast genomes, including even sponges – those metazoans closest to choanoflagellates. Perhaps the ‘birth’ of the original Teneurin occurred in a shared ancestor of M. brevicollis and metazoans, then was lost in M. brevicollis’ sister species, and was serially and repeatedly lost in all diploblast metazoans. Alternatively, and as favored above, it first arose in the ‘urBilaterian,’ then was subsequently acquired from some bilaterian via horizontal transfer by a single choanoflagellate clade. The functional partnership of Teneurins and Latrophilins was discovered in rodents through the LPH1-TENM2 interaction. Recent work extends this to further members of each family. Surveying when the interacting domains of Teneurins and Latrophilins co-exist within different organisms can give an indication of how widespread their functional cooperation might be, across bilaterians. Paralog number for the two families is relatively correlated among bilaterians, and paralog numbers underwent co-increase in the WGDs mentioned above. With co-increasing paralog numbers, the possible combinatorial pairs grow factorially. This should have a significant impact for increasing nervous system complexity. The 3 key events in the ‘natural history’ of the Teneurins and their Latrophilin partners coincide with the ascendance of particularly successful metazoan clades: bilaterians; arthropods; and vertebrates. Perhaps we can attribute some of this success to the unique Teneurin family, and to its partnership with Latrophilins.

Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus

BACKGROUND

In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated.

RESULTS

To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos.

CONCLUSIONS

On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.

Enhancer activities of amphioxus Brachyury genes in embryos of the ascidian, Ciona intestinalis

The notochord and somites are distinctive chordate structures. The T-box transcription factor gene, Brachyury, is expressed in notochord and plays a pivotal role in its formation. In the cephalochordate, Branchiostoma floridae, Brachyury is duplicated into BfBra1 and BfBra2, which are expressed in the somite-formation region as well. In a series of experiments to elucidate the regulatory machinery of chordate Brachyury expression, we carried out a lacZ reporter assay of BfBra in embryos of the urochordate, Ciona intestinalis. Vista analyses suggest the presence of conserved non-coding sequences, not only in the 5'-upstream, but also in the 3'-downstream and in introns of BfBra. We found that: (1) 5'-upstream sequences of both BfBra1 and BfBra2 promote lacZ expression in muscle cells, (2) 3'-downstream sequences have enhancer activity that promotes lacZ expression in notochord cells, and (3) introns of BfBra2 and BfBra1 exhibit lacZ expression preferentially in muscle and notochord cells. These results suggest shared cephalochordate Brachyury enhancer machinery that also works in urochordates. We discuss the results in relation to evolutionary modification of Brachyury expression in formation of chordate-specific organs characteristic of each lineage.

Morphological Stasis and Proteome Innovation in Cephalochordates

Lancelets, extant representatives of basal chordates, are prototypic examples of evolutionary stasis; they preserved a morphology and body-plan most similar to the fossil chordates from the early Cambrian. Such a low level of morphological evolution is in harmony with a low rate of amino acid substitution; cephalochordate proteins were shown to evolve slower than those of the slowest evolving vertebrate, the elephant shark. Surprisingly, a study comparing the predicted proteomes of Chinese amphioxus, Branchiostoma belcheri and the Florida amphioxus, Branchiostoma floridae has led to the conclusion that the rate of creation of novel domain combinations is orders of magnitude greater in lancelets than in any other Metazoa, a finding that contradicts the notion that high rates of protein innovation are usually associated with major evolutionary innovations. Our earlier studies on a representative sample of proteins have provided evidence suggesting that the differences in the domain architectures of predicted proteins of these two lancelet species reflect annotation errors, rather than true innovations. In the present work, we have extended these studies to include a larger sample of genes and two additional lancelet species, Asymmetron lucayanum and Branchiostoma lanceolatum. These analyses have confirmed that the domain architecture differences of orthologous proteins of the four lancelet species are because of errors of gene prediction, the error rate in the given species being inversely related to the quality of the transcriptome dataset that was used to aid gene prediction.

Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage

The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand the dynamics of the gene regulatory network evolution that produced these novelties. We report here the discovery that the cephalochordate lineage possesses two Pax3/7 genes, Pax3/7a and Pax3/7b. The tandem duplication is ancestral to all extant amphioxus, occurring in both Asymmetron and Branchiostoma, but originated after the split from the lineage leading to vertebrates. The two paralogues are differentially expressed during embryonic development, particularly in neural and somitic tissues, suggesting distinct regulation. Our results have implications for the study of amphioxus regeneration, neural plate and crest evolution, and differential tandem paralogue evolution.

Nitric Oxide regulates mouth development in amphioxus

The development of the mouth in animals has fascinated researchers for decades, and a recent study proposed the modern view of recurrent evolution of protostomy and deuterostomy. Here we expanded our knowledge about conserved traits of mouth formation in chordates, testing the hypothesis that nitric oxide (NO) is a potential regulator of this process. In the present work we show for the first time that NO is an essential cell signaling molecule for cephalochordate mouth formation, as previously shown for vertebrates, indicating its conserved ancestral role in chordates. The experimental decrease of NO during early amphioxus Branchiostoma lanceolatum development impaired the formation of the mouth and gill slits, demonstrating that it is a prerequisite in pharyngeal morphogenesis. Our results represent the first step in the understanding of NO physiology in non-vertebrate chordates, opening new evolutionary perspectives into the ancestral importance of NO homeostasis and acquisition of novel biological roles during evolution.