DNA values of four primitive chordates

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114-120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

Genome duplication in early vertebrates: insights from agnathan cytogenetics

Agnathans represent a remnant of a primitive offshoot of the vertebrates, and the long evolutionary separation between their 2 living groups, namely hagfishes and lampreys, could explain profound biological differences, also in karyotypes and genome sizes. Here, cytogenetic studies available on these vertebrates were summarized and data discussed with reference to the recently demonstrated monophyly of this group and to the 2 events of whole genome duplication (1R and 2R) characterizing the evolution of vertebrates. The comparison of cytogenetic data and phylogenetic relationships among agnathans and gnathostomes seems to support the hypothesis that 1R and 2R occurred before the evolutionary divergence between jawless and jawed vertebrates.

Observations on some unusual cell types in the enigmatic worm Xenoturbella (phylum uncertain)

The inner epithelially organized gastrodermis of the enigmatic simple worms of the genus Xenoturbella contains numerous partly phagocytized cells of two kinds, ciliated cells (PCCs) and muscle cells (PMCs). PCCs and PMCs have features of undifferentiated cells and do not derive from differentiated adult cells. Homology of phagocytized cells to pulsatile bodies in acoel and nemertodermatid flatworms is therefore rejected. The phagocytized cells might represent an hitherto unknown process of regeneration in Xenoturbella. The phagocytized material contains as much DNA as in all mitochondria and nuclei of the living cells. This is probably caused by lack of digestion of nucleic acids. The genome size of Xenoturbella bocki was determined. It has a C-value of about 0.55 pg.

Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution

It has been proposed that two events of duplication of the entire genome occurred early in vertebrate history (2R hypothesis). Several phylogenetic studies with a few gene families (mostly Hox genes and proteins from the MHC) have tried to confirm these polyploidization events. However, data from a single locus cannot explain the evolutionary history of a complete genome. To study this 2R hypothesis, we have taken advantage of the phylogenetic position of the lamprey to study the history of gene duplications in vertebrates. We selected most gene families that contain several paralogous genes in vertebrates and for which lamprey genes and an out-group are known in databases. In addition, we isolated members of the nuclear receptor superfamily in lamprey. Hagfish genes were also analyzed and found to confirm the lamprey gene analysis. Consistent with the 2R hypothesis, the phylogenetic analysis of 33 selected gene families, dispersed through the whole genome, revealed that one period of gene duplication arose before the lamprey-gnathostome split and this was followed by a second period of gene duplication after the lamprey-gnathostome split. Nevertheless, our analysis suggests that numerous gene losses and other gene-genome duplications occurred during the evolution of the vertebrate genomes. Thus, the complexity of all the paralogy groups present in vertebrates should be explained by the contribution of genome duplications (2R hypothesis), extra gene duplications, and gene losses.

Gene duplication: past, present and future

Gene duplication is of central interest to evolutionary developmental biology, having been implicated in evolutionary increases in complexity. These ideas stem principally from the Lewis model for the evolution of the BX-C and Ohno's proposal for genome duplications during chordate evolution. Here I revisit these models and show how recent data have confirmed their essential features, but forced some important revisions. These include revised dates for homeotic gene duplications and for widespread gene duplication in vertebrate evolution. I also outline the major unresolved questions in the study of gene duplication, and its relevance to evolution and development.

Developmental regulation and tissue-specific localization of calmodulin mRNA in the protochordate Ciona intestinalis

A full-length cDNA encoding a highly conserved calmodulin was isolated from a cDNA library prepared from hatched larvae of the ascidian Ciona intestinalis. Sequence analysis has identified a 447 b.p. open reading frame, encoding a putative protein of 149 amino acid residues, with a predicted molecular weight of 16.8 kDa, showing 85-98% identity to known calmodulins. Northern blot analysis revealed a single transcript of about 0.8 kb in length, which was maternally expressed and progressively increased during development, until late tail-bud stage. Whole-mount in situ hybridizations, carried out on embryos at different stages of development, showed that starting from the neurula stage, the C. intestinalis calmodulin (Ci-CaM) expression became restricted to the neuroectoderm and that in larvae it was specifically detected in the nervous system.

Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton

Polyploid formation has played a major role in the evolution of many plant and animal genomes; however, surprisingly little is known regarding the subsequent evolution of DNA sequences that become newly united in a common nucleus. Of particular interest is the repetitive DNA fraction, which accounts for most nuclear DNA in higher plants and animals and which can be remarkably different, even in closely related taxa. In one recently formed polyploid, cotton (Gossypium barbadense L.; AD genome), 83 non-cross-hybridizing DNA clones contain dispersed repeats that are estimated to comprise about 24% of the nuclear DNA. Among these, 64 (77%) are largely restricted to diploid taxa containing the larger A genome and collectively account for about half of the difference in DNA content between Old World (A) and New World (D) diploid ancestors of cultivated AD tetraploid cotton. In tetraploid cotton, FISH analysis showed that some A-genome dispersed repeats appear to have spread to D-genome chromosomes. Such spread may also account for the finding that one, and only one, D-genome diploid cotton, Gossypium gossypioides, contains moderate levels of (otherwise) A-genome-specific repeats in addition to normal levels of D-genome repeats. The discovery of A-genome repeats in G. gossypioides adds genome-wide support to a suggestion previously based on evidence from only a single genetic locus that this species may be either the closest living descendant of the New World cotton ancestor, or an adulterated relic of polyploid formation. Spread of dispersed repeats in the early stages of polyploid formation may provide a tag to identify diploid progenitors of a polyploid. Although most repetitive clones do not correspond to known DNA sequences, 4 correspond to known transposons, most contain internal subrepeats, and at least 12 (including 2 of the possible transposons) hybridize to mRNAs expressed at readily discernible levels in cotton seedlings, implicating transposition as one possible mechanism of spread. Integration of molecular, phylogenetic, and cytogenetic analysis of dispersed repetitive DNA may shed new light on evolution of other polyploid genomes, as well as providing valuable landmarks for many aspects of genome analysis.

Presence in invertebrate genomes of sequences characterized by the repetition of the triplet CCPurine

In Drosophila melanogaster (Dm), polypeptidic domains have been found in different morphogenetic genes. Two types of them are characterized by the repetition of nucleotidic triplets: the M repeat (CAX) and the paired repeat (CAXCCX). In this paper we described a third type of repeat isolated from the genome of a Polychaete annelid: Owenia fusiformis. This repeat is characterized by the repetition of the triplet CCPurine. Phylogenetic studies showed the presence of this repeat in all the invertebrate genomes tested (eight copies in Dm genome) while we failed to detect it in vertebrate genomes.

Temporal and spatial expression of a cytoskeletal actin gene in the ascidian Styela clava

We have cloned and characterized the temporal and spatial expression of ScCA15, a cDNA clone encoding an actin gene in the ascidian Styela clava. The partial nucleotide and derived amino acid sequences of this singlecopy gene suggest that it is a cytoskeletal actin. Northern analysis shows that ScCA15 corresponds to a 1.8-kb mRNA that is transcribed during oogenesis, during embryonic development, and in the adult. In situ hybridization shows that maternal ScCA15 mRNA is distributed uniformly in the cytoplasm of the oocyte and unfertilized egg. During the period of ooplasmic segregation following fertilization, however, ScCA15 mRNA appears to be translocated into the ectoplasm, a specialized cytoplasmic region of the egg. During the early cleavages, the ectoplasmic transcripts are partitioned to ectodermal cells in the animal hemisphere, which are precursors of the epidermis and nervous system of the larva. Maternal ScCA15 mRNA is degraded just before gastrulation and replaced by zygotic transcripts which begin to accumulate between the neurula and mid-tailbud stages. Zygotic ScCA15 mRNA accumulates primarily in the epidermal and neural cells, although lower levels of these transcripts may also be present in tail muscle cells. These results show that two mechanisms are used to concentrate ScCA15 mRNA in the ectodermal cells during development: 1) localization and differential segregation of maternal transcripts and 2) specific expression of the ScCA15 gene. ScCA15 mRNA is detected by in situ hybridization in the testes, ovaries, alimentary tract, and endostyle of adults. In the testes, ScCA15 mRNA is present in developing sperm, whereas in the ovary, these transcripts are present in the germinal epithelium and developing oocytes. In the alimentary tract, ScCA15 mRNA is confined to the gastric epithelium of the esophagus, stomach, and intestine. Since the ScCA15 gene is expressed in embryonic and adult tissues that are undergoing rapid cell division, this actin is likely to function in some aspect of cell proliferation.

Genome analysis of Amphioxus and speculation as to the origin of contrasting vertebrate genome organization patterns

1. The genome of Amphioxus was investigated by DNA reassociation techniques for the amount of repetitive and non-repetitive sequences and its pattern of organization. 2. A comparison of the amount of non-repetitive DNA between Amphioxus and the tunicate Ciona intestinalis does not support the hypothesis that the Cephalochordates have arisen from the Tunicates by polyploidy. 3. In the Amphioxus genome repetitive and non-repetitive elements are predominantly arranged in a short period interspersion pattern. Conclusions are presented as to the evolution of contrasting genome organization patterns among vertebrates.

Evolution of isozyme loci and their differential tissue expression. Creatine kinase as a model system

The phylogeny of the creatine kinase (CK, EC 2.7.3.2) isozyme loci and their differential tissue expressions were determined for representatives of 65 families of vertebrates, with emphasis on the fishes. The transition from the single creatine kinase locus, characteristic of certain echinoderms, to the two creatine kinase loci which are orthologous to those present in all vertebrates, occurred early in the chordate line. The majority of pre-teleostean fishes possesses only these two CK loci (A and C). These loci are relatively generalized in their tissue expressions which are variable among species of primitive fishes. The third and fourth creatine kinase loci (B and D) arose separately in the ancestors of the bony fishes and appear to be the result of regional genome duplications. Concomitant with the increase in the number of isozyme loci has been an increase in the specificity of their tissue expression. In the advanced teleost fishes the four CK loci are differentially expressed in a characteristic manner. The A2 isozyme predominates in skeletal muscle, the B2 isozyme in eye and brain, the C2 isozyme in stomach muscle, and the D2 isozyme is found exclusively in testis. We propose a phylogeny of the creatine kinase genes in the lower chordates based on the time of appearance of new CK loci, the sequence in which the loci achieve a tissue restricted expression, and the immunochemical relatedness of the orthologous and paralogous gene products.

Chromosomal changes in vertebrate evolution

The immense variety of karyotypes found in extant species is unmistakable evidence that the process of evolution is associated with karyotypic change. The question whether the chromosome changes are a cause or a consequence of speciation has been debated intensely for many years and, as is often the case with biological problems, there has been no unequivocal answer. Evolution operates along different lines in different groups of organisms. In animals, reproductive biology and population structure are important factors influencing the rate of karyotypic change. Still, the most extreme chromosomal rearrangements are not necessarily found in the most specialized species. A great number of chromosome banding techniques has made it possible to study chromosomes of vertebrates in great detail. Some applications of these techniques to problems of chromosomal polymorphism in relation to mammalian speciation are presented.

A genetic model for the evolution of the glycosphingolipids

The glycosphingolipids have been found in many animal tissues, but the complexity of their molecular structure varies considerably among the different phyla. Relatively simple structures have been found in invertebrate species, while the most complex have been demonstrated in brain tissue of modern fishes and amphibians. The data on the phylogenetic distribution of the glycosphingolipids has been interpreted to indicate that a significant number of gene duplications, involving many different structural genes, may have occurred during a few specific periods of vertebrate evolution. The transition from invertebrate to jawless vertebrate, the divergence of rays and skates from true sharks, the advent of modern bony fishes and the transition from aquatic to terrestrial vertebrates, each could have veen accompained by duplications of genes involved in the synthesis and degradation of glycosphingolipids. The evolutionary study of such a multi-enzyme system may be one means to detect alterations in the genome as a whole. The apparent correspondence in time of these gene duplications involved in glycosphingolipid metabolism and periods of rapid vertebrate evolution which may have been accompanied by significant increases in the amount of cellular DNA suggests that such changes may have occurred via the mechanism of tetraploidization.

Replication of DNA in the chromosomes of eukaryotes

The evidence that each chromatid of a eukaryotic organism contains only one DNA double helix comes from a variety of observations. It begins with the autoradiographic demonstration by J. H. Taylor that tritiated thymidine, incorporated into chromosomes during one round of DNA synthesis, is present in both chromatids at the first division after labelling, but in only one chromatid after a further round of DNA synthesis accomplished in the absence of label. Further evidence comes from those experiments which demonstrate that when two sister chromatids break and fuse one with the other, each chromatid behaves as though it contained two chains of opposite polarity, fusion between chains being restricted to those of like polarity. J. G. Gall’s study of the kinetics of digestion of lampbrush chromosomes by pancreatic DNase also supports the view that each chromatid contains only two polynucleotide chains which are cleaved by this enzyme independently of one another; while O. L. Miller’s observations on the dimensions of the fibres remaining after lampbrush chromosomes have been digested by trypsin only allow for there being two polynucleotide chains per chromatid. By means of the technique of DNA fibre autoradiography devised by J. A. Huberman and A. D. Riggs, the units involved in replicating the chromosomal DNA of somatic cells ofXenopushave been compared with those ofTriturus. Both these organisms have initiation points for DNA replication that are arranged in tandem, and from each initiation point replication proceeds in opposite directions at divergent forks. The intervals between initiation points inXenopusrange from about 20 to 125µm apart, whereas those ofTriturusare much more widely separated. At 25 °C replication of DNA inXenopussomatic cells proceeds at 9µm per hour one-way at each fork, whereas the corresponding rate inTriturusis 20µm per hour.Triturussomatic cells take about 4 times longer than comparable cells ofXenopusto replicate their DNA. TheTriturusgenome contains about 10 times as much DNA as theXenopusgenome, and comparison of the replication process in these two organisms indirectly adds weight to the view that theTriturusgenome is 10 timeslongerthan that ofXenopus, rather than that it contains 10 times as many DNA double helices per chromatid. DNA fibre autoradiography has also been used to study replication inTriturusspermato-cytes. The round of DNA synthesis just before meiosis inTriturusis an exceptionally long-drawn-out process, taking 9 to 10 days for completion at 16 °C. This lengthy S-phase is not occasioned by abnormally slow replication, the rate being 12µm per hour one-way at 18 °C, nor is it the result of an exceptional staggering of replication starts. Instead it appears to be correlated with a gross reduction in the number of initiation points for replication. i.e. with an increase in the lengths of the replicating units. A rough calculation suggests that each meiotic chromomere may correspond to a unit of replication during the pre-meiotic S-phase.