Sister Group Research Articles

Genetic diversity and evolution of the plastome in allotetraploid cotton (Gossypium spp.)

AbstractCotton (Gossypium spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of Gossypium has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted de novo assembly of 336 Gossypium plastomes, mainly from domesticated cultivars, and generated a pan‐plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where Gossypium tomentosum and Gossypium mustelinum formed an early diverging clade rooted by diploids, followed by splitting two sister clades of Gossypium darwinii–Gossypium barbadense and Gossypium hirsutum–Gossypium ekmanianum–Gossypium stephensii. Within the G. hirsutum clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in G. barbadense suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of G. hirsutum was higher than that of G. barbadense. We specifically compared the plastomes of G. hirsutum and G. barbadense to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm.

The Origin of Evergreen Broad-Leaved Forests in East Asia from the Evidence of Floristic Elements.

Arguments about the origin and evolution of the evergreen broad-leaved forests in East Asia exist generally, and are even contradictory in some cases. The origin and evolution of the flora of East Asia, especially in the evolutionary process, the formation time of the Asian monsoon, the implications of phylogenetic and biogeographic studies on some important taxa, and the implications of palaeobotanical evidence are debatable. Most research from different disciplines suggests that the monsoon in the Miocene was key to the diversification of East Asian flora and its evergreen broad-leaved forests. The common view is that the evergreen broad-leaved forests of East Asia are closely related to the monsoon's intensity and developments, which were caused by the uplift of Himalaya-Tibet during or after the mid-Miocene. Analysis of the floristic elements show that the present subtropical evergreen broad-leaved forests in East Asia could have an early or ancient tropical origin and a tropical Asian affinity, but that their species are dominated by endemic Chinese or East Asian ones, many of which have tropical Asian affinity or are tropical sister species. The time of Himalayan uplift and the intensity of the monsoon climate are believed to be key to the formation of the evergreen broad-leaved forests in East Asia. Combined with existing paleobotanical findings, the uplift of the Himalayas and the formation of the monsoon climate, as well as floristic elements of the subtropical evergreen broad-leaved forests, we believe that they evolved from an Asian tropical rainforest after the mid-Miocene in the southeastern region of East Asia, while the ancient subtropical evergreen broad-leaved forests in the southwestern region continuously evolved into the present subtropical ones.

Phylogeny, chronology, and phylogeography in Australasian Hypnodendraceae

Abstract The Hypnodendrales form the sister group to all other pleurcarpous mosses in the superorder Hypnanae. Many species are closely associated with the cool temperate rainforests of Australasia, while others are widespread in higher altitude wet forests across tropical South-East Asia. Several of the Malesian entities are taxonomically ambiguous, having been variously treated as species complexes or as single very variable species. Here we use dated phylogenies to examine the timing of diversification of major clades within the Hypnodendrales, test the hypothesis that widespread, taxonomically problematic species have diversified relatively recently in South-East Asia from within clades of southern temperate origin, and address taxonomic questions within Hypnodendron. A chronogram with broad taxonomic sampling is constructed, followed by a second dated phylogeny with dense sampling from Hypnodendron vitiense, a representative morphologically variable species found throughout Eastern Australia and South-East Asia. The crown group Hypnodendrales are found to have originated in the mid-Cretaceous, although they share a Most Recent Common Ancestor (MRCA) with the other Hypnanae in the late Jurassic. Extant members of Hypnodendron share a MRCA ±28 Mya, a little before the start of the collision of Australia with the Sunda plate that initiated the Australasian–Malesian floristic interchange. Within H. vitiense, there is strong phylogenetic structure consistent with the diversification and isolation of populations in South-East Asia within the last 10 Mya. The New Zealand endemic H. marginatum is found to be derived from within an Australasian clade of H. vitiense, this in turn being distinct from a South-East Asian/tropical Australian H. vitiense clade. Our results suggest that the phylogeography of this prominent group of mosses closely mirrors that of the rainforest ecosystems of which they are a part.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

A new species of the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae) from Phuket Island, Thailand with a discussion of the group’s potential biogeography

Model based integrative analyses supports the recognition of a new species of the Cyrtodactylus brevipalmatus group from Phuket Island, Thailand. Cyrtodactylus thalang sp. nov. is most closely related to the sister species C. brevipalmatus from the Thai-Malay Peninsula and C. cf. brevipalmatus from Langkawi Island, Kedah State, Peninsular Malaysia. Based on the mitochondrial gene ND2, C. thalang sp. nov. bears an uncorrected pairwise sequence divergence of 14.7% and 15.1% from C. cf. brevipalmatus and C. brevipalmatus, respectively, significantly different (p<0.05) mean values of meristic and morphometric characters, and discrete categorical morphological differences. A multiple factor analysis morphospatially statistically placed C. thalang sp. nov. well outside all other species of the brevipalmatus group. The BAYAREALIKE model of a BioGeoBEARS analysis indicated the origin of the brevipalmatus group was in western Indochina with subsequent south to north speciation along the Tenasserim Mountains followed by a west to east invasion of northern Thailand, Laos, and northwestern Vietnam northeast of the Chao Phraya Basin and north of the Khorat Plateau.

A shift between bee and wasp pollinators explains floral divergence in the Duvernoia clade of Justicia (Acanthaceae)

Abstract Floral divergence among sister taxa can arise from pollinator shifts and play a role in speciation. We investigate a potential case of pollinator-driven divergence in the Duvernoia clade of Justicia (Acanthaceae), which includes two species with markedly divergent floral morphology. Pollinator observations and pollen load analyses showed that Justicia aconitiflora is pollinated by vespid wasps, while its sister taxon Justicia adhatodoides is confirmed to be pollinated exclusively by large carpenter bees. Reciprocal nectar-feeding experiments show that wasps and bees are not deterred by the taste of nectar of non-preferred species. Floral morphology matches body and tongue morphology of these two insect groups, and this phenotypic matching mediates pollen transfer and physical access to nectar. Controlled pollination experiments showed that both species are self-compatible, yet dependent on pollinator visits for fruit-set. Historical reconstruction of pollination system evolution in Justicia indicates that the direction of the shift in the Duvernoia clade was from bee to wasp pollinators. This study provides a compelling example of a transition between bee and wasp pollination, and highlights the effects of floral architecture on specialization in plant pollination systems.

The Picocoraciades (hoopoes, rollers, woodpeckers, and allies) from the early Eocene London Clay of Walton-on-the-Naze

We describe upupiform, coraciiform, and possible piciform birds from the early Eocene London Clay of Walton-on-the-Naze (Essex, UK). The material includes partial skeletons of a new species of a small upupiform bird, Waltonirrisor tendringensis, gen. et sp. nov., which is the earliest known representative of the Upupiformes. Three very similar species of stem group rollers are assigned to Laputavis robusta, Septencoracias morsensis, and S. simillimus, sp. nov. These species only differ in minor features, which raises the possibility that the taxon Sepencoracias Bourdon, 2016 is a junior synonym of Laputavis Dyke, 2001. A smaller stem group roller from Walton-on-the-Naze resembles the North American primobucconid species Primobucco mcgrewi. We also describe two species of a new genus-level taxon, Pristineanis, gen. nov., which shows close affinities to the North American “Neanis” kistneri and may be a stem group representative of the Piciformes. In many aspects of their postcranial osteology, the stem group Coracii from Walton-on-the-Naze, as well as the new taxon Pristineanis, resemble coeval Trogoniformes from this fossil site. Because trogons are the extant sister taxon of the Picocoraciades – the clade including the Upupiformes, Coraciiformes, and Piciformes –, the shared similarities are likely to be plesiomorphic for this latter clade. Early Cenozoic representatives of the Upupiformes and Coraciiformes were much smaller than their extant relatives, which suggests that the Picocoraciades are an avian example of Cope’s Rule that postulates a tendency for size increase in evolutionary lineages over time.

Description of a new species of the genus Cultellus Schumacher, 1817 (Bivalvia, Pharidae) from the South China Sea, based on integrative taxonomy

The present study describes a new species within the genus Cultellus Schumacher, 1817 collected from the South China Sea. An integrative taxonomic approach incorporating morphological comparisons, geometric morphometrics and genetic analyses was used to identify and differentiate the new species. Cultellus exilissp. nov. is distinguished from its congeners by its slender, fragile and translucent valves, curved posteroventral margins and relatively large protractor scars. The geometric morphometric analyses, based on outlines data, indicated that samples of Cultellus exilissp. nov. clustered together and were distinctly separated from other species. Multiple species delimitation results, based on the mitochondrial COI gene, support the separation of Cultellus exilissp. nov. from its related congeners. Phylogenetic analyses of a nuclear (28S rRNA) and two mitochondrial (COI, 16S rRNA) genes using Maximum Likelihood and Bayesian Inference methods revealed that the species belongs to the genus Cultellus. The superfamily Solenoidea Lamarck, 1809, which includes the families Solenidae Lamarck, 1809 and Pharidae H. Adams & A. Adams, 1856, exhibits closer affinity to the family Hiatellidae Gray, 1824 than to Solecurtidae d’Orbigny, 1846. Furthermore, we found that the genus Siliqua was clustered alongside the genera Ensiculus and Phaxas as a sister clade, which contradicts the current systematics of the subfamily within the family Pharidae. This work highlights the utility of integrative taxonomy for species identification, recognition and phylogenetic investigation.

Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis

BackgroundThe genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants.ResultsThe lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica’s sister species is Caragana jubata, whereas C. turkestanica’s closest relative is Caragana arborescens.ConclusionsThe present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.

Gyromitra persicula sp. nov. (Discinaceae, Pezizales), a novel discoid Gyromitra from Northwestern North America

Gyromitra persicula (Discinaceae, Pezizales), a new species from Washington state, USA, is described. Like its sister species G. leucoxantha, G. persicula has reticulate ascospores with blunt apiculi that form concave depressions resembling a fishtail. Gyromitra persicula is differentiated from G. leucoxantha by its smaller size, peach to buff coloration, and nrDNA ITS. Further collections are required to better understand the distribution and abundance of this discoid Gyromitra, which is currently only known from a small geographic area of temperate rainforest.

New dinosaur remains increase theropod diversity in the Cañadón Asfalto Formation (Lower Jurassic), Chubut Province, Argentina

The Jurassic record of South American theropods is scarce, being represented by only seven nominal species. Four of these species (Eoabelisaurus mefi, Asfaltovenator vialidadi, Condorraptor currumili and Piatnitzkysaurus floresi) have been found in Toarcian-aged localities in the Cañadón Asfalto Formation (Chubut Province, Argentina) and, as a result, this unit has the highest known diversity of Jurassic theropods on the continent. A dentary with teeth in situ (MPEF-PV 6775) was found close to the base of this formation and differs from the other species from the unit with overlapping morphology. MPEF-PV 6775 resembles the dentary of the Late Jurassic North American theropod Ceratosaurus in being a robust bone, with a strong dorsal curvature in lateral view, and having relatively tall tooth crowns. MPEF-PV 6775 was scored in two matrices that have a broad taxonomic sample focused on Theropoda and the new specimen was recovered in large polytomies with other early neotheropods. A third analysis was conducted scoring MPEF-PV 6775 into a matrix focused in ceratosaurs because of its morphological similarities to Ceratosaurus. In this analysis, MPEF-PV 6775 was recovered as the sister taxon to Ceratosaurus, sharing with the later a ventral margin of the dentary that is strongly convex anteroposteriorly. These results suggest that MPEF-PV 6775 is a ceratosaurian and probably a ceratosaurid. Thus, our results indicate a higher taxonomic diversity of theropods and, in particular, ceratosaurs in the Cañadón Asfalto Formation. MPEF-PV 6775 seems to provide more evidence for the presence of ceratosaurids in the Jurassic of South America, together with isolated teeth described from the Late Jurassic of Uruguay and some analyses that recovered Eoabelisaurus and Berberosaurus within this clade.

 Mazusjiangshiense (Mazaceae), a new species from China: evidence from morphological and molecular analyses.

Utilising both morphological and molecular analyses, this study unveils Mazusjiangshiensesp. nov., a novel addition to the Mazaceae family, discovered in Shaowu County, Fujian Province, China. The comprehensive description and illustrations provided here are a result of a meticulous exploration of its morphological features. While bearing a resemblance to M.gracilis, this new-found species is distinguished by three distinct characteristics: its stems are delicately soft, its leaves possess a membranous quality and the ovary is notably villous at the apex. Integration of molecular evidence, derived from the nuclear ribosomal DNA (nrITS) and three plastid DNA sequences (rps16, rbcL and trnL-trnF), unequivocally supports the classification of M.jiangshiense as a distinct species. Notably, the molecular analysis positions it as a sister species to M.spicatus, underscoring the phylogenetic relationships within the genus Mazus. Our research not only introduces M.jiangshiense as a novel taxonomic entity, but also provides a nuanced understanding of its morphological differences and molecular affinities, enriching our comprehension of the diversity and evolutionary relationships of Mazaceae.

Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii.

SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.

A highly conserved tRNA modification contributes to C. albicans filamentation and virulence.

tRNA modifications play important roles in maintaining translation accuracy in all domains of life. Disruptions in the tRNA modification machinery, especially of the anticodon stem loop, can be lethal for many bacteria and lead to a broad range of phenotypes in baker's yeast. Very little is known about the function of tRNA modifications in host-pathogen interactions, where rapidly changing environments and stresses require fast adaptations. We found that two closely related fungal pathogens of humans, the highly pathogenic Candida albicans and its much less pathogenic sister species, Candida dubliniensis, differ in the function of a tRNA-modifying enzyme. This enzyme, Hma1, exhibits species-specific effects on the ability of the two fungi to grow in the hypha morphology, which is central to their virulence potential. We show that Hma1 has tRNA-threonylcarbamoyladenosine dehydratase activity, and its deletion alters ribosome occupancy, especially at 37°C-the body temperature of the human host. A C. albicans HMA1 deletion mutant also shows defects in adhesion to and invasion into human epithelial cells and shows reduced virulence in a fungal infection model. This links tRNA modifications to host-induced filamentation and virulence of one of the most important fungal pathogens of humans.IMPORTANCEFungal infections are on the rise worldwide, and their global burden on human life and health is frequently underestimated. Among them, the human commensal and opportunistic pathogen, Candida albicans, is one of the major causative agents of severe infections. Its virulence is closely linked to its ability to change morphologies from yeasts to hyphae. Here, this ability is linked-to our knowledge for the first time-to modifications of tRNA and translational efficiency. One tRNA-modifying enzyme, Hma1, plays a specific role in C. albicans and its ability to invade the host. This adds a so-far unknown layer of regulation to the fungal virulence program and offers new potential therapeutic targets to fight fungal infections.

Bouchetaria (Gastropoda: Cypraeidae), a new genus for the Riddle cowry, B. aenigma (Lorenz 2002), from the deep waters of the Mozambique Channel

Based on molecular and conchological features, a new genus, Bouchetaria, is proposed for the Cypraeidae species Nesiocypraea aenigma Lorenz 2002. Molecular analysis of cox1 and 16S genes places Bouchetaria within a monophyletic group—composed of the genera Propustularia, Nesiocypraea, Ipsa, Perisserosa, Cryptocypraea, and Nucleolaria—appearing as the sister group to all other living Cypraeidae. This group corresponds to the Erosariinae (sensu Lorenz & Hubert, 1993). The cox1 pairwise genetic distances between Bouchetaria aenigma and its closest taxa, Propustularia surinamensis and Nesiocypraea teramachii correspond to 15% and 17% difference, respectively. Morphologically, the sole species of the genus Bouchetaria differs from other Erosariinae genera by the near absence of darker color pattern, and denser and longer dentition, which extends onto the labrum and towards the base, where it forms branches. These morphological characters justify the edification of a new genus: Bouchetaria. Consistent with its multispiral protoconch, Bouchetaria aenigma has a fairly wide range in the deep-sea of the Mozambique Channel, from the northern coast of Kwa-Zulu Natal, South Africa, to the northern tip of Madagascar and the Glorioso Islands.

A new genus of scutigerid centipede from southern South America with the description of two new species and an updated molecular phylogeny of the myriapod order Scutigeromorpha (Myriapoda: Chilopoda).

Scutigeromorph centipedes are conspicuous, yet often ignored myriapods for which little work has been conducted in southern South America. After examining recent and museum collections from Chile and Argentina, two new species of generic uncertainty were identified. A new genus of scutigerid centipede, Edgethreua , is therefore described with two new species, E. chilensis from Central Chile (type species of the genus) and E. goloboffi from Argentinian Patagonia. The new genus is characterised by the presence of scattered setiform bristles with short paired spines and the absence of simple spinulae and spines on all stomatotergites, the presence of a single spine-bristle in the prefemur of the second maxilla, a patch of cuticular ridges and pores surrounding the sensilla of the proximal labral portion of the epipharynx, the morphology of the sensilla of the distal patch of the hypopharynx and the morphology of the female gonopods. A phylogenetic analysis of the new species using two nuclear ribosomal RNA genes (18S and 28S rRNA), two mitochondrial ribosomal RNA genes (12S and 16S rRNA) and the mitochondrial protein-encoding gene cytochrome c oxidase subunit I show that the new genus does not cluster with any other described genus of scutigeromorph represented in molecular phylogenies. The data indicate that the new genus is probably sister group to a clade including the genera Lassophora , Ballonema and the subfamily Thereuoneminae, although one analysis suggests a position as sister group to Scutigerinae. ZooBank: urn:lsid:zoobank.org:pub:A4D453F3-9031-4E21-84C7-87F16C07AD51.

Description of Rhipicephalus hibericus sp. nov. (Ixodoidea: Ixodidae), a species of the Rhipicephalus sanguineus group in southwestern Europe

We describe all the life stages of Rhipicephalus hibericus n. sp., provide the types, and present molecular support for a new species of the Rhipicephalus sanguineus sensu lato group, present in southwestern Europe, that has been historically confused with Rhipicephalus turanicus Pomerantzev, 1940. A new name is proposed for this taxon because it was impossible to ascribe to types of already described species in the group, deposited for more than 100 years in natural history institutions. The males have a dorsum showing deep and coarse punctations (absent in Rhipicephalus sanguineus sensu stricto) and adanal plates with large punctations (absent in R. sanguineus s.s.); the tail of the spiracular plate is as wide as the closest festoon (half the width in R. sanguineus s.s.). Females have large punctations in dorsal fields, a wide spiracular plate, and a “V” shaped genital opening; such a combination of characters cannot be found in other species of the group. Immatures are described from specimens collected on hosts (Rodentia and Eulipotyphla). Both larvae and nymphs are markedly smaller than R. sanguineus s.s. Nymphs display long, backward-projected auriculae; larvae are almost half the size of R. sanguineus s.s. The new species can hybridize with R. sanguineus s.s. in laboratory colonies producing an unfertile F2, laying brown and dry eggs that did not hatch. Phylogenetic analysis of partial coxI gene sequences placed R. hibericus in a well-supported clade with other sequences of R. sanguineus s.l. from Portugal, as a sister clade of R. sanguineus s.s. The new species does not belong to the R. turanicus group of species. Both 12S and 16S partial gene sequences were not as precise in the correct phylogenetic placement of R. hibericus, in part probably due to the existence of erroneously identified sequences in GenBank©. This description, together with the previous reinstatement of Rhipicephalus secundus and Rhipicephalus rutilus, and the description of the neotypes of R. sanguineus s.s. should help researchers to adequately identify their collections. Our findings demonstrate that R. turanicus is absent in southwestern Europe. Old collections should be re-examined to provide the actual range of the new species.

The impact of differential transposition activities of autonomous and nonautonomous hAT transposable elements on genome architecture and gene expression in Caenorhabditis inopinata.

Transposable elements are DNA sequences capable of moving within genomes and significantly influence genomic evolution. The nematode Caenorhabditis inopinata exhibits a much higher transposable element copy number than its sister species, Caenorhabditis elegans. In this study, we identified a novel autonomous transposable element belonging to the hAT superfamily from a spontaneous transposable element-insertion mutant in C. inopinata and named this transposon Ci-hAT1. Further bioinformatic analyses uncovered 3 additional autonomous hAT elements-Ci-hAT2, Ci-hAT3, and Ci-hAT4-along with over 1,000 copies of 2 nonautonomous miniature inverted-repeat transposable elements, mCi-hAT1 and mCi-hAT4, likely derived from Ci-hAT1 and Ci-hAT4 through internal deletion. We tracked at least 3 sequential transpositions of Ci-hAT1 over several years. However, the transposition rates of the other 3 autonomous hAT elements were lower, suggesting varying activity levels. Notably, the distribution patterns of the 2 miniature inverted-repeat transposable element families differed significantly: mCi-hAT1 was primarily located in the chromosome arms, a pattern observed in the transposable elements of other Caenorhabditis species, whereas mCi-hAT4 was more evenly distributed across chromosomes. Additionally, interspecific transcriptome analysis indicated that C. inopinata genes with upstream or intronic these miniature inverted-repeat transposable element insertions tend to be more highly expressed than their orthologous genes in C. elegans. These findings highlight the significant role of de-silenced transposable elements in driving the evolution of genomes and transcriptomes, leading to species-specific genetic diversity.

Four new species of Cystolepiota (Agaricaceae, Agaricales) from northeastern China.

Cystolepiota is a tiny lepiotaceous fungi. During our 3 years fieldwork, we found four new species of Cystolepiota from northeastern China. A phylogenetic study of a combined dataset of ITS+nrLSU+rpb2+tef1-α revealed that Cystolepiota changbaishanensis and Cystolepiota hetieri are sister clades; Cystolepiota hongshiensis belongs to Cystolepiota seminuda complex; Cystolepiota luteosquamulosa formed a clade not closely related with any other; Cystolepiota nivalis and Cystolepiota sp. (HMJAU68235) formed a sister clade. All new species are provided with descriptions, photos of the basidiomata, and colored illustrations of the microstructures. A key for the identification of Cystolepiota species from China is also presented.

Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore.

As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.