Phylogenetic relationships of the Mangrove Hummingbird, "Amazilia" boucardi (Apodiformes: Trochilidae) of Costa Rica / Relaciones filogenéticas del Colibrí manglero "Amazilia" boucardi (Apodiformes: Trochilidae) de Costa Rica

Abstract Introduction: A recent revision of the generic classification of the Trochilidae based on DNA sequences revealed many inconsistencies with the current generic classification, largely based on plumage characters subject to homoplasy, especially in the Trochilini, the largest tribe. A thorough generic reorganization brought the classification into accord with the phylogeny, but due to lack of genetic data, two species remained unclassified. One of these was the Mangrove Hummingbird, "Amazilia" boucardi, endemic to Costa Rica and included in the IUCN red list of threatened species. Objective: To obtain molecular evidence to clarify the generic relationships of "A." boucardi. Methods: We isolated DNA from tissues of this species and amplified 4 nuclear and 4 mitochondrial fragments and compared these with homologous fragments from 56 species in the Trochilini, constructing phylogenetic trees with maximum likelihood and Bayesian methods. Results: Our phylogenetic analyses confirmed the placement of boucardi in the Trochilini and definitely excluded it from Amazilia but placed it with high confidence in the genus Chrysuronia Bonaparte, 1850, within which its closest relative is C. coeruleogularis, which also inhabits mangroves. Conclusions: Our genetic data based on nuclear and mitochondrial regions clearly indicate the relationship of A. boucardi and L. coeruleogularis. Moreover, it is also supported by their habitat distribution in the mangroves of the Pacific coast of Costa Rica and Western Panama. Therefore, we suggested to exclude A. boucardi as "incertae sedis".

Resumen Introducción: Una revisión reciente de la clasificación de la familia Trochilidae con base en secuencias de ADN demostró muchas incongruencias con la clasificación genérica previa, que había sido hecho con base en caracteres del plumaje muy sujetos a homoplasia, especialmente en la tribu más grande, Trochillini. Una reorganización de los géneros logró llevar su clasificación genérica a la concordancia con la filogenia, pero debido a la ausencia de datos genéticos, dos especies permanecieron sin clasificar. Una de estas fue el colibrí de manglar Amazilia boucardi, una especie endémica de Costa Rica, considerada como amenazada en la lista roja de la UICN. Objetivo: Obtener evidencia molecular para esclarecer las relaciones genéricas de A. boucardi. Métodos: Se aisló ADN de tejidos de esta especie y se amplificaron 4 fragmentos de ADN del núcleo y 5 de la mitocondria, y se compararon con fragmentos homólogos de 56 especies en la tribu Trochillini, generando árboles filogenéticos con métodos de máxima verosimilitud y bayesiano. Resultados: Los análisis filogénticos obtenidos confirmaron la ubicación de boucardi en Trochilini y definitivamente la excluyó del género Amazilia, pero la ubicó con un alto grado de confianza en el género Chrysuronia Bonaparte, 1850, dentro los cuales su pariente más cercano es C. coeruleogularis, que también habita manglares. Conclusiones: Nuestros datos genéticos basados en regiones nucleares y mitocondriales indican claramente la relación entre A. boucardi and L. coeruleogularis. Es más, lo anterior se sustenta por su distribución en los manglares de la costa Pacífica de Costa Rica y oeste de Panamá. Por lo tanto, sugerimos excluir a A. boucardi como "incertae sedis".

Identification of homologs of the Chlamydia trachomatis effector CteG reveals a family of Chlamydiaceae type III secreted proteins that can be delivered into host cells.

Chlamydiae are a large group of obligate endosymbionts of eukaryotes that includes the Chlamydiaceae family, comprising several animal pathogens. Among Chlamydiaceae, Chlamydia trachomatis causes widespread ocular and urogenital infections in humans. Like many bacterial pathogens, all Chlamydiae manipulate host cells by injecting them with type III secretion effector proteins. We previously characterized the C. trachomatis effector CteG, which localizes at the host cell Golgi and plasma membrane during distinct phases of the chlamydial infectious cycle. Here, we show that CteG is a Chlamydiaceae-specific effector with over 60 homologs phylogenetically categorized into two distinct clades (CteG I and CteG II) and exhibiting several inparalogs and outparalogs. Notably, cteG I homologs are syntenic to C. trachomatis cteG, whereas cteG II homologs are syntenic among themselves but not with C. trachomatis cteG. This indicates a complex evolution of cteG homologs, which is unique among C. trachomatis effectors, marked by numerous events of gene duplication and loss. Despite relatively modest sequence conservation, nearly all tested CteG I and CteG II proteins were identified as type III secretion substrates using Yersinia as a heterologous bacterial host. Moreover, most of the type III secreted CteG I and CteG II homologs were delivered by C. trachomatis into host cells, where they localized at the Golgi region and cell periphery. Overall, this provided insights into the evolution of bacterial effectors and revealed a Chlamydiaceae family of type III secreted proteins that underwent substantial divergence during evolution while conserving the capacity to localize at specific host cell compartments.

Phylogenetic relationships and systematics of tapeworms of the family Davaineidae (Cestoda, Cyclophyllidea), with emphasis on species in rodents.

The present study aims at clarifying the poorly known phylogenetic relationships and systematics of cestodes of the family Davaineidae Braun, 1900 (Cyclophyllidea), primarily the genus Raillietina Fuhrmann, 1920 and of the subfamily Inermicapsiferinae (Anoplocephalidae) from mammals (mostly rodents, 31 new isolates) and birds (eight new isolates). Phylogenetic analyses are based on sequences of the large subunit ribosomal RNA gene (28S) and mitochondrial NADH dehydrogenase subunit 1 gene (nad1). The main phylogenetic pattern emerging from the present analysis is the presence of three independent lineages within the main clade of the subfamily Davaineinae, one of which is almost entirely confined to species from rodents and the other two show a mixture of species from birds and mammals. It is suggested that the major diversification of the main clade took place in birds, possibly in galliforms. The subsequent diversification included repeated host shifts from birds to mammals and to other birds, and from rodents to other mammals, showing that colonisation of new host lineages has been the main driver in the diversification of davaineine cestodes. It is also shown that all isolates of Inermicapsifer Janicki, 1910, mainly from rodents, form a monophyletic group positioned among Raillietina spp. in the "rodent lineage", indicating that the genus Inermicapsifer is a member of the family Davaineidae. This means that the subfamily Inermicapsiferinae and the family Inermicapsiferidae should be treated as synonyms of the Davaineidae, specifically the subfamily Davaineinae. Three additional genera generally included in the Inermicapsiferinae, i.e. Metacapsifer Spasskii, 1951, Pericapsifer Spasskii, 1951 and Thysanotaenia Beddard, 1911, are also assigned here to the Davaineidae (subfamily Davaineinae). Raillietina spp. were present in all three main lineages and appeared as multiple independent sublineages from bird and mammalian hosts, verifying the non-monophyly of the genus Raillietina and suggesting a presence of multiple new species and genera.

Comparative mitochondrial genome analysis provides new insights into the classification of Modiolinae.

BACKGROUND: Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. Currently, the position of Modiolinae within Mytilidae and the taxonomic and phylogenetic relationships within Modiolinae were still controversial. This study focuses on the complete mitochondrial genomes of two species: Modiolus modulaides (Röding, 1798) and Modiolus auriculatus Krauss, 1848, which have not been sequenced before. METHODS AND RESULTS: We assembled and characterized the mitochondrial genomes of M. modulaides and M. auriculatus and then analyzed the phylogenetic relationships. The mitochondrial genomes of M. modulaides and M. auriculatus were 15,422 bp and 16,027 bp, respectively. Both of them were composed of 36 functional genes, including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. All protein-coding genes showed A + T bias, positive GC skews, and negative AT skews in nucleotide composition. Phylogenetic analysis based on the mitochondrial genomes showed that Modiolinae and Bathymodiolinae clustered together to form a sister relationship. Seven Modiolinae species were divided into two clades: L1 (M. modulaides, M. auriculatus and Modiolus philippinarum Hanley, 1843) and L2 [Modiolus modiolus (Linnaeus, 1758), Modiolus kurilensis Bernard, 1983, Modiolus nipponicus (Oyama, 1950), and Modiolus comptus (Sowerby III, 1915)]. The divergence time of the two clades was approximately 105.75 Ma. Furthermore, the transfer RNA gene rearrangement, longer genetic distance, and greater genetic differentiation were confirmed between the L1 and L2 clades, as well as differences in the external characteristics of the shells of the two clades. CONCLUSIONS: Based on the molecular data, it was speculated that species from the L1 clade might belong to other genera or new genera. This study provides molecular information for further taxonomic and phylogenetic studies of Mytilidae.

New insights into the early morphological evolution of sea turtles by re-investigation of Nichollsemys baieri, a three-dimensionally preserved fossil stem chelonioid from the Campanian of Alberta, Canada.

The early evolution of Pan-Chelonioidea (sea turtles) is poorly understood. This is in part due to the rarity of undeformed skulls of definitive early stem chelonioids. In this work, we redescribe the holotype of Nichollsemys baieri using µCT scans and segmentations of the skull. This fossil is the best 3D preserved skull of any Campanian sea turtle, and includes partial "soft tissue" preservation. Nichollsemys is morphologically similar but clearly distinct from Toxochelys spp., and both show a mosaic of plesiomorphic and derived chelonioid features. The internal cranial anatomy documents the presence of derived characters in Nichollsemys baieri that are absent in Toxochelys spp., such as the loss of the epipterygoids and the rod-like shape of the rostrum basisphenoidale. Among the numerous plesiomorphic characters is the presence of a splenial bone, which was unnoticed before. An updated phylogenetic analysis retrieves Nichollsemys baieri as a non-protostegid early stem chelonioid in a slightly more crownward position than Toxochelys latiremis. Our phylogeny includes macrobaenids and protostegids as pan-chelonioids, and we find unorthodox results for dermochelyids. Thus, although Nichollsemys baieri provides important new insights into the early morphological evolution of sea turtles, much work remains to be done. As a completely 3D preserved specimen, we included Nichollsemys baieri into a recent landmark-based skull shape dataset of turtles. Morphospace analysis reveals an intermediate position between cryptodires and crown chelonioids. Based on these data, we also predict that Nichollsemys baieri was still capable of neck retraction, constraining the loss of this trait to more crownward pan-chelonioids. Supplementary Information: The online version contains supplementary material available at 10.1186/s13358-024-00323-8.

The Systematics of the Trematoda.

The platyhelminth class Trematoda comprises two subclasses with largely disparate species diversity, with the small Aspidogastrea with c.80 species and the speciose Digenea with c.18,000 species, which has attracted much effort towards our understanding of evolutionary relationships among suprageneric taxa. This chapter focuses on insights into the classification of the Digenea, that have become apparent from our advanced understanding of both morphological and molecular data. The field of molecular systematics of the Digenea has experienced significant advances over the past 15 years. Phylogenetic analyses of sequence data predominantly from the 18S and 28S rRNA genes have incorporated a considerable diversity of taxa, thus increasing the accuracy of phylogenetic inferences at higher taxonomic levels. As a result, the status of long-standing supraspecific taxa has been revised, new higher-level taxa have been defined, and inferences made in association with morphological and life-cycle evidence. A substantial effort has been made towards a classification reflecting a natural system of the Digenea by considering morphological evidence in conjunction with phylogenies inferred from molecular data; this has resulted in considerable congruence. However, limited taxon sampling in the phylogeny of the Digenea still remains relevant, especially in relation to some higher-level taxa, and an outline of these omissions is presented. A framework that has led to robust estimates of phylogeny is outlined, and the application of advanced morphological and molecular approaches in digenean taxonomy and systematics is illustrated using the most comprehensively studied digenean superfamilies.

Methylobacterium amylolyticum sp. nov. and Methylobacterium ligniniphilum sp. nov., isolated from soil.

Two pink-pigmented bacteria, designated strains NEAU-140T and NEAU-KT, were isolated from field soil collected from Linyi, Shandong Province, PR China. Both isolates were aerobic, Gram-stain-negative, rod-shaped, and facultatively methylotrophic. 16S rRNA gene sequences analysis showed that these two strains belong to the genus Methylobacterium. Strain NEAU-140T exhibited high 16S rRNA gene sequence similarities to Methylobacterium radiotolerans NBRC 15690T (97.43 %) and Methylobacterium phyllostachyos NBRC 105206T (97.36 %). Strain NEAU-KT exhibited high 16S rRNA gene sequence similarities to M. phyllostachyos NBRC 105206T (99.00 %) and Methylobacterium longum DSM 23933T (98.72 %). A phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-140T formed a clade with Methylobacterium aerolatum (95.94 %), Methylobacterium persicinum (95.66 %) and Methylobacterium komagatae (96.87 %), and strain NEAU-KT formed a cluster with M. phyllostachyos and M. longum. The predominant fatty acid in both strains was C18 : 1 ω7c. Both strains contained ubiquinone Q-10 as the only respiratory quinone. The polar lipid profiles of both strains contained diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. Whole-genome phylogeny showed that strains NEAU-140T and NEAU-KT formed a phyletic line with M. aerolatum, M. persicinum, Methylobacterium radiotolerans, Methylobacterium fujisawaense, Methylobacterium oryzae, Methylobacterium tardum, M. longum and M. phyllostachyos. The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NEAU-140T and its closely related strains were lower than 82.62 and 25.90  %, respectively. The ANI and dDDH values between strain NEAU-KT and its closely related strains were lower than 86.29 and 31.7 %, respectively. The genomic DNA G+C contents were 71.63 mol% for strain NEAU-140T and 69.08 mol% for strain NEAU-KT. On the basis of their phenotypic and phylogenetic distinctiveness and the results of dDDH and ANI hybridization, these two isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium amylolyticum sp. nov. (type strain NEAU-140T=MCCC 1K08801T=DSM 110568T) and Methylobacterium ligniniphilum sp. nov. (type strain NEAU-KT=MCCC 1K08800T=DSM 110567T) are proposed.

The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea.

We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome  and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.

Solving the Myxidium rhodei (Myxozoa) puzzle: insights into its phylogeny and host specificity in Cypriniformes.

Myxidium rhodei Léger, 1905 (Cnidaria: Myxozoa) is a kidney-infecting myxosporean that was originally described from the European bitterling Rhodeus amarus. Subsequently, it has been documented based on spore morphology in more than 40 other cypriniform species, with the roach Rutilus rutilus being the most commonly reported host. This study introduces the first comprehensive data assessment of M. rhodei, conducted through morphological, ecological and molecular methods. The morphological and phylogenetic analyses of SSU rDNA sequences of Myxidium isolates obtained from European bitterling and roach did not support parasite conspecificity from these fish. In fact, the roach-infecting isolates represent three distinct parasite species. The first two, M. rutili n. sp. and M. rutilusi n. sp., are closely related cryptic species clustering with other myxosporeans in the freshwater urinary clade, sharing the same tissue tropism. The third one, M. batuevae n. sp., previously assigned to M. cf. rhodei, clustered in the hepatic biliary clade sister to bitterling-infecting M. rhodei. Our examination of diverse cypriniform fishes, coupled with molecular and morphological analyses, allowed us to untangle the cryptic species nature of M. rhodei and discover the existence of novel species. This underscores the largely undiscovered range of myxozoan diversity and highlights the need to incorporate sequence data in diagnosing novel species.

Title: Résoudre le casse-tête de Myxidium rhodei (Myxozoa) : aperçu de sa phylogénie et de sa spécificité d'hôte chez les Cypriniformes. Abstract: Myxidium rhodei Léger, 1905 (Cnidaria : Myxozoa) est un Myxosporea infectant les reins qui a été décrit à l'origine chez la bouvière, Rhodeus amarus. Par la suite, il a été documenté, sur la base de la morphologie des spores, chez plus de 40 autres espèces de cypriniformes, le gardon Rutilus rutilus étant l'hôte le plus fréquemment signalé. Cette étude présente la première évaluation complète des données sur M. rhodei, réalisée par des méthodes morphologiques, écologiques et moléculaires. Les analyse morphologiques et phylogénétiques des séquences d'ADNr SSU des isolats de Myxidium obtenus à partir de bouvières et de gardons européens n'ont pas confirmé la conspécificité du parasite de ces poissons. En fait, les isolats infectant les gardons représentent trois espèces distinctes de parasites. Les deux premières, M. rutili n. sp. et M. rutilusi n. sp., sont des espèces cryptiques étroitement apparentées, regroupées avec d'autres Myxosporea du clade urinaire d'eau douce, partageant le même tropisme tissulaire. La troisième, M. batuevae n. sp., précédemment attribuée à M. cf. rhodei, appartient au clade biliaire hépatique, groupe-frère de M. rhodei infectant la bouvière. Notre examen de divers poissons cypriniformes, couplé à des analyses moléculaires et morphologiques, nous a permis de démêler la nature cryptique des espèces de M. rhodei et de découvrir l'existence de nouvelles espèces. Cela souligne la diversité largement méconnue des Myxozoaires et souligne la nécessité d'incorporer des données de séquence dans le diagnostic de nouvelles espèces.

D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy.

Introduction: Porcine circovirus 2 (PCV-2) is a key pathogen for the swine industry at a global level. Nine genotypes, differing in epidemiology and potentially virulence, emerged over time, with PCV-2a, -2b, and -2d being the most widespread and clinically relevant. Conversely, the distribution of minor genotypes appears geographically and temporally restricted, suggesting lower virulence and different epidemiological drivers. In 2022, PCV-2e, the most genetically and phenotypically divergent genotype, was identified in multiple rural farms in North-eastern Italy. Since rural pigs often have access to outdoor environment, the introduction from wild boars was investigated. Methods: Through a molecular and spatial approach, this study investigated the epidemiology and genetic diversity of PCV-2 in 122 wild boars across different provinces of North-eastern Italy. Results: Molecular analysis revealed a high PCV-2 frequency (81.1%, 99/122), and classified the majority of strains as PCV-2d (96.3%, 78/81), with sporadic occurrences of PCV-2a (1.2%, 1/81) and PCV-2b (2.5%, 2/81) genotypes. A viral flow directed primarily from domestic pigs to wild boars was estimated by phylogenetic and phylodynamic analyses. Discussion: These findings attested that the genotype replacement so far described only in the Italian domestic swine sector occurred also in wild boars. and suggested that the current heterogeneity of PCV-2d strains in Italian wild boars likely depends more on different introduction events from the domestic population rather than the presence of independent evolutionary pressures. While this might suggest PCV-2 circulation in wild boars having a marginal impact in the industrial sector, the sharing of PCV-2d strains across distinct wild populations, in absence of a consistent geographical pattern, suggests a complex interplay between domestic and wild pig populations, emphasizing the importance of improved biosecurity measures to mitigate the risk of pathogen transmission.

Characterization of CRESS-DNA viruses in human vaginal secretions: An exploratory metagenomic investigation.

The Phylum Cressdnaviricota consists of a large number of circular Rep-encoding single-stranded (CRESS)-DNA viruses. Recently, metagenomic analyzes revealed their ubiquitous distribution in a diverse range of eukaryotes. Data relating to CRESS-DNA viruses in humans remains scarce. Our study investigated the presence and genetic diversity of CRESS-DNA viruses in human vaginal secretions. Vaginal swabs were collected from 28 women between 29 and 43 years old attending a fertility clinic in New York City. An exploratory metagenomic analysis was performed and detection of CRESS-DNA viruses was confirmed through analysis of near full-length sequences of the viral isolates. A phylogenetic tree was based on the REP open reading frame sequences of the CRESS-DNA virus genome. Eleven nearly complete CRESS-DNA viral genomes were identified in 16 (57.1%) women. There were no associations between the presence of these viruses and any demographic or clinical parameters. Phylogenetic analysis indicated that one of the sequences belonged to the genus Gemycircularvirus within the Genomoviridae family, while ten sequences represented previously unclassified species of CRESS-DNA viruses. Novel species of CRESS-DNA viruses are present in the vaginal tract of adult women. Although they be transient commensal agents, the potential clinical implications for their presence at this site cannot be dismissed.

Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length.

Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43-4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield.

Molecular Identification of a New Species of Absidia (Cunninghamellaceae, Mucorales) Isolated from Soil in Korea.

The species within the family Cunninghamellaceae during an investigation of soil microfungi in Korea, in which three strains were isolated from Gangwon, Chungbuk, and Gyeongbuk provinces, designated as KNUF-22-121A, KNUF-22-126A, and KNUF-22-316, respectively. Because the morphological and molecular analyses of these three strains were identical, KNUF-22-316 underwent further detailed study. Phylogenetic analyses based on the concatenated nucleotide sequences of the internal transcribed spacer region and the large subunit 28S rRNA gene revealed that the strain belonged to the genus Absidia, but occupied a distinct phylogenetic position. The strain KNUF-22-316 was compared with closely related species Absidia radiata CGMCC 3.16257T and Absidia yunnanensis CGMCC 3.16259T, morphologically different with shorter sporangiophores, smaller sporangia and columellae, and the consistent presence of collars. Here, we provide a detailed description and images of this proposed new species, which we have named Absidia microsporangia sp. nov.

Three novel woody litter inhabiting fungi in Didymosphaeriaceae, Phaeoseptaceae and Synnemasporellaceae from Zhujiangyuan Nature Reserve, Yunnan Province, P.R. China.

Zhujiangyuan Nature Reserve, located in Qujing City, Yunnan Province, China, is reported with high fauna and floral diversity, while the fungal diversity of the region is poorly documented. During the summer season in 2023, decaying wood-inhabiting microfungi were collected from different microhabitats. The novel species were identified based on morphological characteristics and phylogenetic analyses (based on combined datasets of ITS, LSU, SSU, tef1-α, and rpb2 regions). Two species belong to Dothideomycetes (viz., Spegazziniazhujiangyuanensis sp. nov. and Phaeoseptumzhujiangyuanense sp. nov. in Pleosporales) while the other one resides in Sordariomycetes (Synnemasporellafanii sp. nov. in Diaporthales). The results are in conformity with the earlier studies that predicted higher fungal diversity in this region.

Bottlebrush and Myrtle twig canker caused by Neopestalotiopsis species: an emerging canker-causing group of fungi in Italy.

Pestalotioid fungi were isolated in pure culture from symptomatic plants of Callistemonlaevis, C.viminalis, Lumaapiculata (marketed as "Myrtusluma"), Myrtuscommunissubsp.tarentina, and M.communisvar.microphylla (M.communis 'Microphylla'), showing twig canker, dieback and defoliation. The isolates were identified to species by ITS, tef1 and tub2 sequences, which revealed the presence of six species of Neopestalotiopsis (N.camelliae-oleiferae, N.hispanica, N.iberica, N.rosae, N.rosicola, and N.zakeelii) and one species of Pestalotiopsis (P.biciliata). While most species were isolated only once or twice, the majority of isolates belonged to N.rosae (13) and N.hispanica (8). Pathogenicity was investigated by pathogenicity tests on all hosts, which confirmed the pathogenicity of all Neopestalotiopsis species on at least some of the hosts tested, while P.biciliata did not cause any disease symptoms. Neopestalotiopsishispanica and N.rosae caused symptoms in all hosts of the present study, while the other Neopestalotiopsis species tested showed no symptoms on Lumaapiculata.

Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastreadeformis, from Japan and northern Taiwan.

A new zooxanthellate scleractinian coral, Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Scleractinia, Merulinidae), is described from non-coral reef regions of Japan and northern Taiwan. This new species was previously recognized as a morphological variant of Paragoniastreadeformis (Veron, 1990) and can be morphologically distinguished from that species by lacking groove-and-tube structures on corallite wall joints, and by having larger calices, numerous septa, and up to three corallites in one valley. The new species also formed an independent clade from its congeners, P.australensis (Milne Edwards & Haime, 1857), P.deformis and P.russelli (Wells, 1954), in the molecular phylogeny based on the mitochondrial intergenic region and nuclear ribosomal internal transcribed spacers.

The complete chloroplast genome of the Syzygium buxifolium Hook. Et Arn.1833 and its phylogenetic analysis.

Syzygium buxifolium. Hook. Et Arn.1833 is a member of the Myrtaceae family. This species is used in traditional Chinese medicines. It possesses numerous synonyms, reflecting the ambiguity in its taxonomy. The chloroplast genome has been widely used for species identification and phylogenetic analysis. Regrettably, there is a lack of information regarding the chloroplast genome of S. buxifolium. Here, we intend to obtain the chloroplast genome of S. buxifolium to resolve its classification problems. In particular, we utilized Illumina sequencing technology to sequence, GetOrganelle to assemble, and CPGAVAS2 to characterize the chloroplast genome of S. buxifolium. The chloroplast genome of S. buxifolium had a length of 158,581 bp and consisted of 111 unique genes, comprising 78 protein-coding genes, 29 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. In addition, we identified 86 Simple Sequence Repeats, 345 tandem repetitive sequences, and 34 dispersed repetitive sequences using modules implemented in CPGAVAS2. Lastly, we carried out phylogenetic analysis using Phylosuite. The results indicated a close relationship between S. buxifolium and S. grijsii. This study offers novel genetic data for the molecular identification and subsequent phylogenetic analysis of the Syzygium genus.

Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem.

Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.

A multiscale analysis of coralline algae Lithophylloideae (Corallinophycidae, Rhodophyta) shedding new light on understanding cryptic diversity.

Cryptic diversity abounds in many biological species, posing challenges to our understanding of biological diversity, conservation and management. Taking the common coralline algae, the subfamily Lithophylloideae as an illustration, this study delved into the implications of cryptic diversity through global-level phylogenetic and geographical analysis based upon Lithophylloideae molecular data worldwide, as well as a multi-locus time-calibrated phylogeny to elucidate their possible evolutionary process. The multiscale analysis revealed the polyphyly in current concept of the genus Lithophyllum. Geographic isolation resulting from the Tethys terminal event (TTE) has led to two distinct distribution regions for this so-called cosmopolitan genus: one regionally distributed along European coasts/Mediterranean that should include the taxonomical Lithophyllum; others widely distributed, particularly among pan-tropic waters, suggesting at least five groups to be rediscovered within the subfamily Lithophylloideae. Meanwhile, the cryptic genus Titanoderma, lacking morphological identification features with Lithophyllum, exhibited differences in distribution and evolutionary patterns consistent with their ecological habits, thus supporting their separation. This study provided useful hints for cryptic diversity, which advocated an integrative thinking to investigating global cryptic diversity and exploring the broad linkages between phylogenetic relationships and evolutionary origin, biogeography, morphological and ecological traits to achieve a more comprehensive understanding of biodiversity.

SUPPLEMENTAL DESCRIPTION OF CABALLEROTREMA ANNULATUM (DIESING, 1850) OSTROWSKI DE NÚÑEZ AND SATTMANN, 2002 (DIGENEA: CABALLEROTREMATIDAE) FROM A NEW HOST (ELECTROPHORUS CF. VARII) AND LOCALITY (AMAZON RIVER, COLOMBIA) WITH PHYLOGENETIC ANALYSIS AND EMENDED GENERIC DIAGNOSIS.

Herein, we provide a supplemental description of Caballerotrema annulatum (Diesing, 1850) Ostrowski de Núñez and Sattmann, 2002 (Digenea: Caballerotrematidae Tkach, Kudlai, and Kostadinova, 2016) based on specimens collected from the intestine of an electric eel, Electrophorus cf. varii (Gymnotiformes: Gymnotidae) captured in the Amazon River (Colombia). This caballerotrematid can be differentiated from its congeners by the following combination of morphological features: body surface spines forming contiguous transverse rows, concentric (wrapping dorso-ventrally around body), distributing into posterior body half (vs. restricted to anterior body half in Caballerotrema brasiliensePrudhoe, 1960; indeterminate for Caballerotrema aruanenseThatcher, 1980 and Caballerotrema piscicola [Stunkard, 1960] Kostadinova and Gibson, 2001); head collar lacking projections (vs. having them in C. brasiliense, C. aruanense, and C. piscicola), narrow (head collar more narrow than maximum body width vs. the head collar being obviously wider than the body in C. brasiliense, C. aruanense, and C. piscicola); corner spines clustered (vs. corner spines distributing as 2 separated pairs in C. brasiliense, C. aruanense, and C. piscicola); pharynx approximately at level of the corner spines (vs. pharynx far anterior to corner spines in C. brasiliense, C. aruanense, and C. piscicola); and testes ovoid and nonoverlapping (C. aruanense; vs. sinuous and overlapping in C. brasiliense and C. piscicola). Based on our results, we revise the diagnosis of CaballerotremaPrudhoe, 1960 to include features associated with the shape and distribution of body surface spines, orientation and position of head collar spines, cirrus sac, seminal vesicle, oviduct, Laurer's canal, oötype, vitellarium, and transverse vitelline ducts. We performed Bayesian inference analyses using the partial large subunit ribosomal (28S) DNA gene. Our 28S sequence of C. annulatum was recovered sister to that of Caballerotrema sp. (which is the only other caballerotrematid sequence available in GenBank) from an arapaima, Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Peruvian Amazon. Our sequence of C. annulatum comprises the only caballerotrematid sequenced tethered to a morphological description and a voucher specimen in a lending museum. The present study is a new host record and new locality record for C. annulatum. The phylogeny comprises the most resolved and taxon-rich evolutionary hypothesis for Echinostomatoidea published to date.