Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution

The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.     

Suppressor of Hairless and Presenilin phenotypes imply involvement of canonical Notch-signalling in segmentation of the spider Cupiennius salei

Arthropods, vertebrates, and annelids all have a segmented body. Our recent discovery of involvement of Notch-signalling in spider segmentation revived the discussion on the origin of segmented body plans and suggests the sharing of a common genetic program in a common ancestor. Here, we analysed the spider homologues of the Suppressor of Hairless and Presenilin genes, which encode components of the canonical Notch-pathway, to further explore the role of Notch-signalling in spider segmentation. RNAi silencing of two spider Suppressor of Hairless homologues and the spider Presenilin homologue causes severe segmentation phenotypes. The most prominent defect is the consistent breakdown of segmentation after the formation of three (Suppressor of Hairless) or five (Presenilin) opisthosomal segments. These phenotypes indicate that Notch-signalling during spider segmentation likely involves the canonical pathway via Presenilin and Suppressor of Hairless. Furthermore, it implies that Notch-signalling influences both the formation and patterning of the spider segments: it is required for the specification of the posterior segments and for proper specification of the segment boundaries. We argue that alternative, partly redundant, pathways might act in the formation of the anterior segments that are not active in the posterior segments. This suggests that at least some differences exist in the specification of anterior and posterior segments of the spider, a finding that may be valid for most short germ arthropods. Our data provide additional evidence for the similarities of Notch-signalling in spider segmentation and vertebrate somitogenesis and strengthen our previous notion that the formation of the segments in arthropods and vertebrates might have shared a genetic program in a common ancestor.     

Genome Duplication and Gene Loss Affect the Evolution of Heat Shock Transcription Factor Genes in Legumes

Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species.     

Early embryonic development in the spider Achaearanea tepidariorum: Microinjection verifies that cellularization is complete before the blastoderm stage

The spider Achaearanea tepidariorum is emerging as a non-insect model for studying developmental biology. However, the availability of microinjection into early embryos of this spider has not been reported. We defined the early embryonic stages in A. tepidariorum and applied microinjection to its embryos. During the preblastoderm 16- and 32-nucleus stages, the energids were moving toward the egg periphery. When fluorochrome-conjugated dextran was microinjected into the peripheral region of 16-nucleus stage embryos, it was often incorporated into a single energid and inherited in the progeny without leaking out to surrounding energids. This suggested that 16-nucleus stage embryos consisted of compartments, each containing a single energid. These compartments were considered to be separate cells. Fluorochrome-conjugated dextran could be introduced into single cells of 16- to 128-nucleus stage embryos, allowing us to track cell fate and movement. Injection with mRNA encoding a nuclear localization signal/green fluorescent protein fusion construct demonstrated exogenous expression of the protein in live spider embryos. We propose that use of microinjection will facilitate studies of spider development. Furthermore, these data imply that in contrast to the Drosophila syncytial blastoderm embryo, the cell-based structure of the Achaearanea blastoderm embryo restricts diffusion of cytoplasmic gene products.     

Gene duplication,genome duplication,and the functional diversification of vertebrate globins

The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α₂β₂). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.     

A new specimen ofWeinbergina opitzi (Chelicerata: Xiphosura) from the Lower Devonian Hunsriick Slate, Germany

A new specimen of the synziphosurine arthropodWeinbergina opitzi is described from the Lower Devonian (Lower Emsian) Hunsrück Slate of Germany (Rhenish Slate Mountains). It is the smallest and only the fifth specimen of this taxon to be described and is preserved in ventral aspect with exceptional preservation of prosomal and opisthosomal appendages. This specimen confirms the presence of a seventh appendage, similar in morphology to the preceding prosomal appendages, associated with opisthosomal segment one. In addition, at least three opisthosomal plates fringed with teeth are confirmed. Correlation of prosomal appendage podomeres betweenWeinbergina and selected chelicerate taxa shows that appendage structure is most similar to eurypterid appendages III–IV and Araneae appendages III–VI. This is in contrast to modern horseshoe crabs which have fewer podomeres in appendages II–V due to an undifferentiated tibiotarsus.      

The delineation of the fourth walking leg segment is temporally linked to posterior segmentation in the mite Archegozetes longisetosus (Acari: Oribatida,Trhypochthoniidae)

Acari (mites and ticks) lack external segmentation, with the only indication of segmentation being the appendages of the prosoma (chelicerae, pedipalps, and four pairs of walking legs). Acari also have a mode of development in which the formation of the fourth walking leg is suppressed until the nymphal stages, following a hexapodal larva. To determine the number of segments in the posterior body region (opisthosoma) of mites, and to also determine when the fourth walking leg segment is delineated during embryogenesis, we followed the development of segmentation in the oribatid mite Archegozetes longisetosus using time‐lapse and scanning electron microscopy, as well as in situ hybridizations of the A. longisetosus orthologues of the segmentation genes engrailed and hedgehog. Our data show that A. longisetosus patterns only two opisthosomal segments, indicating a large degree of segmental fusion or loss. Also, we show that the formation of the fourth walking leg segment is temporally tied to opisthosomal segmentation, the first such observation in any arachnid.     

Embryonic expression patterns of Wnt genes in the RTA-clade spider Cupiennius salei

Spiders represent widely used model organisms for chelicerate and even arthropod development and evolution. Wnt genes are important and evolutionary conserved factors that control and regulate numerous developmental processes. Recent studies comprehensively investigated the complement and expression of spider Wnt genes revealing conserved as well as diverged aspects of their expression and thus (likely) function among different groups of spiders representing Mygalomorphae (tarantulas), and both main groups of Araneae (true spiders) (Haplogynae/Synspermiata and Entelegynae). The allegedly most modern/derived group of entelegyne spiders is represented by the RTA-clade of which no comprehensive data on Wnt expression were available prior to this study. Here, we investigated the embryonic expression of all Wnt genes of the RTA-clade spider Cupiennius salei. We found that most of the Wnt expression patterns are conserved between Cupiennius and other spiders, especially more basally branching species. Surprisingly, most differences in Wnt gene expression are seen in the common model spider Parasteatoda tepidariorum (a non-RTA clade entelegyne species). These results show that data and conclusions drawn from research on one member of a group of animals (or any other organism) cannot necessarily be extrapolated to the group as a whole, and instead highlight the need for comprehensive taxon sampling.     

Comparative genome mapping reveals evidence of gene conversion between Sox9 paralogs of rainbow trout (Oncorhynchus mykiss)

Considerable evidence suggests that one genome duplication event preceded the divergence of teleost fishes and a second genome duplication event occurred before the radiation of teleosts of the family Salmonidae. Two Sox9 genes have been isolated from a number of teleosts and are called Sox9a and Sox9b. Two Sox9 gene copies have also been isolated from rainbow trout, a salmonid fish and are called Sox9 and Sox9α2. Previous evaluations of the evolutionary history of rainbow trout Sox9 gene copies using phylogenetic reconstructions of their coding regions indicated that they both belong to the Sox9b clade. In this study, we determine the true evolutionary history of Sox9 gene copies in rainbow trout. We show that the locus referred to as Sox9 in rainbow trout is itself duplicated. Mapping of the duplicated Sox9 gene copies indicates that they are co-orthologs of Sox9b while mapping of Sox9α2 indicates that it is an ortholog of Sox9a. This relationship is supported by phylogenetic reconstruction of Sox9 gene copies in teleosts using their 3′ untranslated regions. The conflicting phylogenetic topology of Sox9 genes in rainbow trout indicates the occurrence of gene conversion events between Sox9 and Sox9α2 which is supported by a number of recombination analyses.     

Early development of the anterior body region of the grey widow spider Latrodectus geometricus Koch, 1841 (Theridiidae, Araneae)

We document the early morphogenesis of Latrodectus geometricus, particularly of the anterior body region. Significant changes in the development of the external prosomal structures revealed with scanning electron microscopy (SEM) images include: (1) reorganisation of each pre-cheliceral lobe by subdivision and internalisation of its central area; (2) shortening of the ventro-median bridge connecting the pre-cheliceral lobes and its eventual disappearance; (3) appearance and expansion of a prospective mouth region between the pre-cheliceral lobes with a recessed median area surrounded by lip-like borders, the anterior lip-part developing into the hypostome; (4) reduction of the mouth region to an area around the hypostome and the lip-like latero-posterior border of the mouth opening; (5) change of the position of the mouth region from anterior to the insertions of the chelicerae to posterior to them; (6) eventual shortening of the mouth opening to a slit overhung by the hypostome; (7) origination of the prosomal shield from the anterior margin of the pre-cheliceral lobes and the tergal portions of the four posterior-most prosomal segments; and (8) expansion of a ‘ventral sulcus’ from the cheliceral to the fifth opisthosomal segment separating the sides of these segments. Embryonic features are compared across the Chelicerata and discussed briefly in a phylogenetic context.     

Function and molecular evolution of mammalian Sox15, a singleton in the SoxG group of transcription factors

In mammals, the group G of the Sry-related high-mobility-group (HMG) box genes (Sox) contains only one member, Sox15. Comparative genomic analysis of the Sox genes in the B1 and G groups indicates that an ancestral gene may have originated as an intron-containing gene belonging to group B1 and evolved into zebrafish Sox19a/b, Xenopus SoxD, and mammalian Sox15. Although these genes have different names, they are orthologous. The zebrafish and Xenopus orthologues are highly expressed in the central nervous system, whereas mouse Sox15 only shows strong expression in the placenta, an organ characteristic of all mammals except monotremes. Interestingly, Sox15 appears to be a pseudogene in the marsupial opossum. Sox15-deficient mice exhibit delayed skeletal muscle regeneration, indicating that Sox15 plays a crucial role in this process. On the other hand, Xenopus SoxD induces anterior neural development. Thus, there appears to be little functional overlap between Sox15 and its orthologues, Sox19a/b and SoxD. In this review, I discuss the roles of Sox15, its functional redundancy with SoxB1 group members, and its molecular evolution.