Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia

The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.

Genetic Characterization of Small Ruminant Lentiviruses Isolated from Dairy Sheep in Greece

The high genetic heterogeneity of small ruminant lentiviruses (SRLV) renders the genetic characterization of the circulating strains crucial for the epidemiological investigation and the designation of effective diagnostic tools. In Greece, research data regarding the genetic diversity of the circulating SRLV strains is scarce, hindering the implementation of efficient surveillance and control programs. The objective of the study was to genetically characterize SRLV strains isolated from intensive dairy sheep farms in Greece and evaluate the variability of the immunodominant regions of the capsid protein. For this reason, a total of 12 SRLV-infected animals from four intensive dairy sheep farms with purebred Chios and Lacaune ewes were used for the amplification and sequencing of an 800 bp gag-pol fragment. The phylogenetic analyses revealed a breed-related circulation of strains; Chios ewes were infected with strains belonging exclusively to a separate group of genotype A, whereas strains belonging to subtype B2 were isolated from Lacaune ewes. Immunodominant epitopes of capsid protein were quite conserved among the strains of the same genotype, except for the Major Homology Region which showed some unique mutations with potential effects on viral evolution. The present study contributes to the extension of the current knowledge regarding the genetic diversity of SRLV strains circulating in sheep in Greece. However, broader genetic characterization studies are warranted for the exploration of possible recombinant events and the more comprehensive classification of the circulating strains.

Species diversity and taxonomy of Vararia (Russulales, Basidiomycota) with descriptions of six species from Southwestern China

Vararia is a species-rich genus in the family Peniophoraceae and has been shown to be polyphyletic. In this study, sequences of ITS and LSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed with the maximum likelihood, maximum parsimony, and Bayesian inference methods. Seventeen lineages including six new species from China, i.e., V.fissurata, V.lincangensis, V.punctata, V.isabellina, V.sinensis, and V.yaoshanensis were recognized, in which V.fissurata is characterized by the brittle basidiomata with pruinose and cracking hymenophore having white to olivaceous buff hymenial surface, the clamped generative hyphae, presence of the two types gloeocystidia; V.lincangensis is characterized by the simple-septa generative hyphae, and thick-walled skeletal hyphae, and ellipsoid basidiospores; V.punctata is delimited by its thin to slightly thick-walled generative hyphae, and thick-walled skeletal hyphae, present thick-walled, clavate to cylindrical gloeocystidia; V.isabellina is characterized by having the cream to isabelline to slightly brown hymenial surface, thin to slightly thick-walled generative hyphae, and sub-fusiform to navicular basidiospores; V.sinensis is distinguishable by its white to slightly pink hymenial surface, thick-walled skeletal hyphae, and sub-fusiform to navicular basidiospores; V.yaoshanensis is characterized by cream to pinkish buff to cinnamon-buff hymenial surface, slightly thick-walled generative hyphae, the presence of two types gloeocystidia, and slightly thick-walled, ellipsoid basidiospores. Phylogram based on the ITS+nLSU rDNA gene regions included nine genera within the family Peniophoraceae as Amylostereum, Asterostroma, Baltazaria, Dichostereum, Michenera, Peniophora, Scytinostroma and Vararia, in which the six new wood-inhabiting fungi species were grouped into genus Vararia. The phylogenetic tree inferred from the combined ITS and LSU tree sequences highlighted that V.fissurata was found to be the sister to V.ellipsospora with strong supports. Additionally, V.lincangensis was clustered with V.fragilis. Furthermore, V.punctata was retrieved as a sister to V.ambigua. Moreover, V.sinensis was grouped with five taxa as V.breviphysa, V.pirispora, V.fusispora, V.abortiphysa and V.insolita. The new species V.isabellina formed a monophyletic lineage, in which it was then grouped closely with V.daweishanensis, and V.gracilispora. In addition, V.yaoshanensis was found to be the sister to V.gallica with strong supports. The present results increased the knowledge of Vararia species diversity and taxonomy of corticioid fungi in China. An identification key to 17 species of Vararia in China is provided.

Epicoccum sorghinum Causing Leaf Spot on Polygonatum cyrtonema in China

Polygonatum cyrtonema Hua (family Asparagaceae) is a traditional Chinese medicinal plant that is widely cultivated in various parts of China, including Hunan Province. In summer 2022, a leaf spot disease was observed in 10% of the P. cyrtonema plants (Huang jing) in 18 hectares of this crop in the Hongjiang District (27°18'4″N, 110°11'1″E) of Hunan Province. The initial symptoms of the disease were brown spots on young leaves, and adjacent tissues gradually changed from green to yellow. The entire leaf then became yellow, withered, and eventually exhibited a thn and black appearance. In total, 12 diseased plants from four sampling sites (three plants per site) were collected for laboratory analysis to address the concerns of P. cyrtonema growers. Symptomatic leaf samples were selected, and the leaf fragments containing infected parts of the plants were disinfected with 75% ethanol for 1 min, then immersed in 2.5% hypochlorite for 45 s. After disinfection, symptomatic leaf samples were rinsed three times with sterile water, placed on potato saccharose agar containing 50 μg/ml kanamycin and incubated at 25°C for 2 days. Subsequently, 12 fungal isolates were isolated from various leaf samples through hyphal tip transferring. Ten of the 12 fungal isolates had similar morphological features, and one of them (isolate hjh) was used as the representative isolate for the study. With a growth rate of 6.3 mm per day, its white colonies transformed into red concentric rings in five days; they gradually became black after 10 days of growth. The chlamydospores were round (4.0-9.9 × 3.1-9.3 µm, n = 30), whereas the conidia were ovate (8.0-12.1 × 3.2-6.5 µm, n = 30). The morphological features of the isolate hjh were similar to the features of Epicoccum spp. (Aveskamp et al. 2010). The internal transcribed spacer (ITS) region (including the partial ITS1 sequence and the 5.8S and ITS2 complete sequences), β-tubulin (tub) gene, and large subunit (LSU) rRNA gene, were amplified from the isolate hjh using the primer pairs ITS5/ITS4, Bt2a/Bt2b, and LROR/LR5, respectively (Taguiam et al. 2021). BLASTn analysis showed that the ITS (OR253745), tub (OR253764), and LSU (OR253746) sequences generated from the isolate hjh were 98-99% similar to the sequences of E. sorghinum strains CBS 179.80 and CBS 627.68. Subsequently, the ITS, tub, and LSU sequences were combined using Sequence Matrix software; phylogenetic analysis via Bayesian and maximum likelihood methods (Vaidya et al. 2011; Li et al. 2021) classified the isolate hjh into the E. sorghinum clade. To fulfill Koch's postulates, pathogenicity tests were conducted on healthy (lesion-free and disease-free) 2-year-old P. cyrtonema plants. Three healthy plants were inoculated by spraying whole plant until run-off with a spore suspension of the isolate hjh (1 × 106 conidia/ml); Three other healthy plants were sprayed with sterile water as controls. The inoculated plants were incubated in a growth chamber at 25 ± 2°C with 85% humidity for 28 days(Chen et al. 2021). Leaves from the inoculated plants gradually became brown within 15 days. Finally, the plants died 28 days after inoculation. The control plants showed no symptoms throughout the experimental period. Isolates (isolate hjh1, hjh2 and hjh3) that were reisolated from the inoculated plants exhibited morphologically similar characteristics and molecularly identical to the original isolate hjh. To our knowledge, this is the first report of E. sorghinum causing leaf spot disease on P. cyrtonema. The results of this study may facilitate the production of P. cyrtonema in China.

First Report on Apothecium Deformity of Morchella importuna Caused by Alternaria alternata in China

Morel mushrooms (Morchella spp.) are highly regarded globally for their distinctive texture and savory flavor. In 2022, the cultivation area for morel mushrooms in China reached nearly 20,000 hectares, with predominant cultivars including M. sextelata, M. importuna and M. exima (Bian et al., 2024). In March 2022, however, deformities of friting bodies were observed in M. importna at morel mushroom farms in Huaihua city (28.43°N, 110.47°), China, with an incidence rate ranging from 5% to 10%. The disease symptoms begin with the invasion of the hymenium of morel mushroom by white cotton-like mycelia, ultimately resulting in halted fruiting body growth and the manifestation of anomalous fruiting body morphology. Infected samples were collected from the morel growers. Following sterilization with 75% ethanol of the surrounding tissue of infected samples, the white hyphae from the morel lesions were picked out using a dissecting needle, and incubated onto potato saccharose agar medium supplemented with 60 mg/L streptomycin at 25°C. Studies showed that seven out of nine fungal isolates exhibiting identical morphological features rapidly grew on the same culture medium described above, reaching a length of 75 mm in 4 to 5 days at 25°C. The white and thick hyphal colonies of these isolates gradually filled with brown spore powder. Generally, the conidia of the hyphal colonies were polyblastic with protrusions at the tips, measuring 75 to 165 × 36 to 50 μm (n = 30) in width and length, displaying colors varying from light reddish brown to grayish brown, and possessing one or five septa. To confirm the identity of the pathogen, the region of the internal transcribed spacer region (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II second largest subunit (rpb2) genes of the representative isolate H2 were amplified by PCR (Taguiam, et al. 2021). The generated ITS (OR338304), rpb2 (OR452112) and LSU (OR338334) from the isolate H2 had 98-100% similarity to the Alternaria alternata strains ATCC 6663 and CBS 880.95 in BLASTn analysis. ITS, rpb2 and LSU sequences were assembled using Sequence Matrix, and their homogeneity was assessed with PAUP (Vaidya et al., 2011). Bayesian (MrBayes-3.2.7a) and maximum-likelihood (RAxML1.3.1) methods, utilizing the best fit GTR+G+I model obtained from MrModeltest 2.3, were employed for phylogenetic analysis (Aveskamp et al. 2010). Based on morphological characteristics and phylogenetic analysis, the isolate H2 was identified as A. alternata. In the second year post-disease, disease-free morels, with a height of 3 cm, were cultivated in field greenhouses and used for test. A 15 ml suspension (1 × 106 conidia/ml) was applied to 15 young fruiting bodies and their corresponding substrate soil. The results showed that the reappearance of white cotton-like mycelia and deformed M. importuna fruiting bodies within 7 days post-inoculation with the spore suspension, as opposed to the controls. The isolates (H2-1, H2-2 and H2-3) were reisolated from the infected tissues and identified as A. alternata based on its morphological features and phylogenetic analyses. In this study, a similar investigation was previously conducted on cultivated quinoa (Chenopodium quinoa) in Eastern Denmark (Colque-Little et al., 2023). This study marks the first documentation of A. alternata causing deformities in M. importuna fruiting bodies. These deformities occur under conditions of high-temperature (>22°C) and high humidity (>88%). Our findings provide crucial insights for managing A. alternata in M. importuna cultivation in China.

Complete mitochondrial genome of the Starhead Topminnow Fundulus dispar (Cyprinodontiformes: Fundulidae)

Topminnows of the Teleost genus Fundulus serve as model organisms in ecotoxicology because of their broad physiological tolerance and propensity to breed in captivity. This research has been primarily limited to intraspecific comparisons, due to incomplete understanding of the evolutionary history of the genus, which is necessary for use of phylogenetic comparative methods. Interspecific relationships of topminnows remain unresolved, despite recent advances in mitochondrial and nuclear genome sequencing. Specifically, interrelationships of a group containing the starhead topminnows (Fundulus blairae, F. dispar, F. escambiae, F. lineolatus, and F. nottii) typically yield low node support values. Here, we present the first annotated mitochondrial genome of the Starhead Topminnow (F. dispar) and provide a phylogenetic hypothesis for starhead topminnows within the genus Fundulus. DNA was isolated from a specimen of F. dispar collected in Kentucky, USA. The circular genome is 16,564 bp long and contains 13 protein-coding genes, two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA), and one control region (D-loop). Our phylogenetic analysis supports a sister relationship between F. dispar and a group containing F. notatus and F. olivaceus. This data helps to resolve the phylogenetic placement of starhead topminnows.

The second complete mitochondrial genome of Capillidium rhysosporum within the family Capillidiaceae, Entomophthorales

The complete mitochondrial genome of the entomophthoroid fungus Capillidium rhysosporum (strain no.: ATCC 12588) was sequenced using next-generation sequencing technology. The assembled circular genome has a length of 46,756 base pairs with a GC content of 27.06%. Gene prediction identified 15 core protein-coding genes (PCGs), two rRNA genes, and 27 tRNA genes. Phylogenetic analysis confirmed that C. rhysosporum belongs to the Zoopagomycota clade and is closely related to C. heterosporum. This study presents the second complete mitochondrial genome within the family Capillidiaceae, contributing to the mitochondrial DNA database of entomophthoroid fungi.

Diversity of Wickerhamomyces (Wickerhamomycetaceae, Saccharomycetales) in China with the description of four new species

Wickerhamomyces is a well-known genus of the family Wickerhamomycetaceae in the class Ascomycetes. These fungi can survive in a variety of substrates and environments and perform many valuable roles in both industrial processes and the natural ecosystems. During our investigation of yeast diversity associated with plant materials, 53 Wickerhamomyces isolates were obtained from rotting wood and plant leaves collected in Fujian, Guizhou, Henan, and Yunnan Provinces of China. Isolates were identified as 14 Wickerhamomyces species, including 1 species known previously to occur in China (W. anomalus), 9 new record species in China (W. arborarius, W. ciferrii, W. edaphicus, W. lynferdii, W. pijperi, W. subpelliculosa, W. xylosica, W. strasburgensis, and W. sydowiorum), and 4 novel species (W. guiyangensis sp. nov., W. paramyanmarensis sp. nov., W. quanzhouensis sp. nov., and W. phyllophilus sp. nov.). This study presents a detailed account of these new species, illustrating their morphology and analyzing their phylogenetic relationships with other Wickerhamomyces species. Our study is the first comprehensive study on Wickerhamomyces species associated with plant materials from tropical and subtropical China. The results of this study update our understanding of the phylogenetic relationships, systematics, and ecology of Wickerhamomyces.

The complete chloroplast genome sequence of Jacobaea cannabifolia

Jacobaea cannabifolia is a widely used medicinal plant. The total length of the chloroplast genome was 151,390 bp, and it comprised a large single-copy (LSC, 83,432 bp) region, a small single-copy (SSC, 18,304 bp) region, and a pair of inverted repeats (IRs, 49,654 bp). A total of 130 coding genes were annotated, including 88 protein-coding genes, 8 rRNA genes, and 34 tRNA genes. A phylogenetic tree was showed that J. cannabifolia and other species of the same genus clustered together.

Species diversity and major host/substrate associations of the genus Akanthomyces (Hypocreales, Cordycipitaceae)

Akanthomyces, a group of fungi with rich morphological and ecological diversity in Cordycipitaceae (Ascomycota, Hypocreales), has a wide distribution amongst diverse habitats. By surveying arthropod-pathogenic fungi in China and Southeast Asia over the last six years, nine Akanthomyces spp. were found and identified. Five of these were shown to represent four known species and an undetermined species of Akanthomyces. Four of these were new species and they were named A.kunmingensis and A.subaraneicola from China, A.laosensis from Laos and A.pseudonoctuidarum from Thailand. The new species were described and illustrated according to the morphological characteristics and molecular data. Akanthomycesaraneogenus, which was isolated from spiders from different regions in China, Thailand and Vietnam, was described as a newly-recorded species from Thailand and Vietnam. The phylogenetic positions of the nine species were evaluated, based on phylogenetic inferences according to five loci, namely, ITS, nrLSU, TEF, RPB1 and RPB2. In this study, we reviewed the research progress achieved for Akanthomyces regarding its taxonomy, species diversity, geographic distribution and major host/substrate associations. The morphological characteristics of 35 species in Akanthomyces, including four novel species and 31 known taxa, were also compared.

Single-cell DNA from West Greenland marine sediments suggests presence of Protoperidinium tricingulatum in the Arctic

Spiny brown dinoflagellate cysts are commonly used as sea-ice indicators in the Arctic, but their biological affinities are not well known. We present the first indication of hitherto temperate Protoperidinium tricingulatum in the Arctic based on single-cell LSU rDNA sequencing from sediments of the Disko Bay-Vaigat Sound, West Greenland. The morphological similarity of the sequenced cyst morphotype to the sea-ice indicator Islandinium? cezare morphotype 1 is striking. The morphology of the isolated cysts, as well as those observed in the total cyst assemblage following standard palynological preparation, both resemble either I.? cezare morphotype 1 or P. tricingulatum, suggesting that the specimens may in fact be close morphological variants of the same species. In addition, nine LSU rDNA sequences were obtained from morphological variants assigned to Islandinium minutum s.l.: including both subspecies minutum and subspecies barbatum. The two subspecies could not be differentiated based on partial LSU rDNA sequencing. Overall, Arctic spiny brown dinoflagellate cyst species may be morphologically more diverse and taxonomically more complex than shown earlier and further genetic and morphological studies are needed. Importantly, the value of cysts as palaeoecological indicators depends on a sound understanding of their biological affinity and taxonomy.

The phylogeny and taxonomy of Upretia (Caloplacoideae, Teloschistaceae), reveal three new species from Southwestern China

Several specimens of Upretia from Southwest China are morphologically and phylogenetically distinct from currently recognized species in the genus. These specimens are here accommodated within a new species, Upretiazeorina Li J. Li & Printzen. It is characterized by an areolate to squamulose thallus with brown to blackish brown upper surface, pruinose, zeorine type apothecia, black discs, narrowly bacilliform conidia, and the production of gyrophoric acid. Two other specimens of Upretia from China are distinct from currently accepted species and tentatively referred to as Upretia sp. 1 and Upretia sp. 2. A key to all known species of Upretia is also provided.

Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, Shewanella zhuhaiensis sp. nov., Isolated from a Tidal Flat Sediment

A new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26T isolated from Qi'ao Island's tidal flat sediment was identified. Strain 3B26T can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were identified as iso-C15:0, referred to as summed feature 3, and C16:0; the polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and phospholipid; and the quinones contained Q-7, Q-8, MK-7, and MMK7. The genomic size of strain 3B26T was 4,682,650 bp, and its genomic DNA G + C content was 54.8%. While a 16S rRNA gene-based phylogenetic analysis confirmed that strain 3B26T belongs to the genus Shewanella, both phylogenomic inference and genomic comparison revealed that strain 3B26T is distinguishable from its relatives, and digital DNA-DNA hybridization (dDDH) values of 24.4-62.6% and average nucleotide identities (ANIs) of 83.5-95.6% between them were below the 70% dDDH and 96% ANI thresholds for bacterial species delineation. Genomic functional analysis demonstrated that strain 3B26T possesses complete gene clusters of eicosapentaenoic acid biosynthesis and denitrification. Based on the evidence above, strain 3B26T is considered to represent a novel species of the genus Shewanella, and the name Shewanella zhuhaiensis sp. nov. (type strain 3B26T = GDMCC 1.2057T = KCTC 82339T) is proposed.

Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologuskungweensis, L.meleagris, L.ornatipinnis, Neolamprologusbrevis, N.caudopunctatus, N.leleupi, and N.similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A + T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A + T content was higher than the G + C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L.meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species.

Molecular Survey of Rickettsia raoultii in Ticks Infesting Livestock from Pakistan with Notes on Pathogen Distribution in Palearctic and Oriental Regions

Ticks are hematophagous ectoparasites that transmit different pathogens such as Rickettsia spp. to domestic and wild animals as well as humans. Genetic characterizations of Rickettsia spp. from different regions of Pakistan are mostly based on one or two genetic markers and are confined to small sampling areas and limited host ranges. Therefore, this study aimed to molecularly screen and genetically characterize Rickettsia spp. in various tick species infesting camels, sheep, and goats. All the collected tick specimens were morphologically identified, and randomly selected tick species (148) were screened molecularly for the detection of Rickettsia spp. by amplifying three rickettsial DNA fragments, namely, the citrate-synthase gene (gltA), outer-membrane protein A (ompA), and outer-membrane protein B (ompB). After examining 261 hosts, 161 (61.7%) hosts were found infested by 564 ticks, including 287 (50.9%) nymphs, 171 (30.3%) females, and 106 (18.8%) males in five districts (Kohat, Dera Ismail Khan, Lower Dir, Bajaur, and Mansehra). The highest occurrence was noted for Hyalomma dromedarii (number = 72, 12.8%), followed by Haemaphysalis sulcata (n = 70, 12.4%), Rhipicephalus turanicus (n = 64, 11.3%), Rhipicephalus microplus (n = 55, 9.7%), Haemaphysalis cornupunctata (n = 49, 8.7%), Hyalomma turanicum (n = 48, 8.5%), Hyalomma isaaci (n = 45, 8.0%), Haemaphysalis montgomeryi (n = 44, 7.8%), Hyalomma anatolicum (n = 42, 7.5%), Haemaphysalis bispinosa (n = 38, 6.7%), and Rhipicephalus haemaphysaloides (n = 37, 6.6%). A subset of 148 ticks were tested, in which eight (5.4%) ticks, including four Hy. turanicum, two Ha. cornupunctata, one Ha. montgomeryi, and one Ha. bispinosa, were found positive for Rickettsia sp. The gltA, ompA, and ompB sequences revealed 100% identity and were phylogenetically clustered with Rickettsia raoultii reported in China, Russia, USA, Turkey, Denmark, Austria, Italy, and France. Additionally, various reports on R. raoultii from Palearctic and Oriental regions were summarized in this study. To the best of our knowledge, this is the first report regarding genetic characterization and phylogenetic analysis of R. raoultii from Pakistan. Further studies to investigate the association between Rickettsia spp. and ticks should be encouraged to apprise effective management of zoonotic consequences.

A new species of Xenophrys (Amphibia, Anura, Megophryidae) from southern Tibet, China

A new species of Xenophrys is described from Yadong County, Tibet Autonomous Region, China based on morphological and molecular evidence. Phylogenetic analyses based on the mitochondrial genes 16S rRNA and COI indicated that this new species represents an independent lineage and the minimum p-distance based on 16S rRNA between this species and its congeners is 4.4%. Additionally, the new species is distinguished from its congeners by a combination of the following morphological characters: (1) small body size, SVL 17.9-22.2 mm in adult males and SVL 23.4 mm in the single adult female; (2) tympanum indistinct, supratympanic fold distinct; (3) canthus rostralis well-developed, snout tip far beyond the margin of the lower lip; (5) pupil vertical; (6) vomerine teeth present, maxillary teeth present; (7) tongue notched posteriorly; (8) supernumerary tubercles absent, subarticular, metacarpal and metatarsal tubercles indistinct; (9) relative finger lengths I < II < IV < III, finger tips rounded, slightly expanded relative to digit widths; (10) toes with narrow lateral fringes and tarsal folds; (11) a dark triangular marking with light edge between eyes, a dark ")("-shaped marking, with light edge, present on center of dorsum, pectoral glands on sides of the breast.

Update on the genus Robertmurraya: a bacterial genus honoring Dr. Robert G.E. Murray (with some personal reminiscences)

The genus Robertmurraya was created by my group in 2020 to recognize the contributions of Dr. Robert G.E. Murray to the field of prokaryotic taxonomy. This manuscript updates the information regarding this genus. In addition to the seven Robertmurraya species with validly published names, the work presented here shows that two species with effectively published names, "Bacillus yapensis" and "Bacillus dakarensis", and an uncharacterized Bacillus sp. Y1 are also affiliated with this genus. Based on these results, reclassification of "Bacillus yapensis" as a novel species Robertmurraya yapensis sp. nov. is proposed. It is also suggested that "Bacillus dakarensis", for which strains are not available from culture collections, should also be recognized as "Robertmurraya dakarensis". This article also reflects on the serendipitous way I came to know Dr. Murray and his extensive interactions with me and strong support for our work for more than 10 years. Dr. Murray also introduced me and our work to his friend and contemporary Dr. Peter Sneath, who like him also contributed extensively to the field of prokaryotic taxonomy. This introduction led to a fruitful collaboration with Dr. Sneath leading to a joint publication describing the use of the Character Compatibility approach to molecular sequence data.

Helicobacter zhangjianzhongii sp. nov., isolated from dog feces

In 2019, two distinct bacterial isolates were independently isolated from the fecal samples of separate dogs in Beijing, China. These cells exhibit microaerobic, are Gram-negative, motile, and possess a characteristic spiral shape with bipolar single flagellum. They display positive results for the oxidase test while being negative for both catalase and urease. These organisms measure approximately 0.2-0.3 μm in width and 4.5-6 μm in length. The colonies are wet, flat, grey, circular, and smooth with sizes ranging from 1 to 2 mm in diameter after 2 days of growth. However, strains may exhibit variations in size and morphology following extended incubation. Phylogenetic analyses based on the 16S rRNA gene and core genome indicated that these two isolates belong to the genus Helicobacter and formed a robust clade that was remains distinctly separate from currently recognized species. These two isolates shared low dDDH relatedness and ANI values with their closest species Helicobacter canis CCUG 32756T, with these values falling below the commonly cutoff values for strains of the same species. The genomic DNA G + C contents of strain XJK30-2 were 44.93 mol%. Comparing the phenotypic and phylogenetic features between these two isolates and their closely related species, XJK30-2 represents a novel species within the genus Helicobacter, for which the name Helicobacter zhangjianzhongii sp. nov. (Type strain XJK30-2T = GDMCC 1.3695T) is proposed.

Characterization of the complete chloroplast genome of Cynanchum acutum subsp. sibiricum (Apocynaceae)

In this study, we assembled the complete chloroplast (cp) genome of Cynanchum acutum subsp. sibiricum using high-throughput Illumina sequencing reads. The resulting chloroplast genome assembly displayed a typical quadripartite structure with a total length of 158,283 bp, which contained a pair of inverted repeat regions (IRs) of 24,459 bp. These two IRs were separated by a large single-copy region (LSC) and a small single-copy region (SSC) of 89,424 bp and 19,941 bp in length, respectively. The C. acutum subsp. sibiricum cp genome contained 130 genes, and its overall GC content was 37.87%. Phylogenetic analysis among C. acutum subsp. sibiricum and nine other Cynanchum species demonstrated that C. acutum subsp. sibiricum was closely related to C. chinense. The C. acutum subsp. sibiricum cp genome presented in this study lays a good foundation for further genetic and genomic studies of the Cynanchum as well as Apocynaceae.

Phenotypic and Genomic Characteristics of Campylobacter gastrosuis sp. nov. Isolated from the Stomachs of Pigs in Beijing

Campylobacter is among the four main causes of gastroenteritis worldwide. Most reported Campylobacter infections are caused by C. jejuni and C. coli. However, other emerging Campylobacter pathogens have been recognized as important pathogens in humans and animals. A novel bacterial strain, PS10T, was isolated from the gastric mucous of pigs in 2022 in Beijing, China. The cell was Gram-negative, microaerobic, motile, and negative for catalase, oxidase, and urease. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and core genome indicated that this isolate belongs to the genus Campylobacter. There were low dDDH relatedness and ANI values shared within this strain and its closest species C. mucosalis below the cut-off values generally recognized for isolates of the same species. The draft genome size of PS10T is 2,240,910 bp in length with a percentage of DNA G+C contents of 37.72%. Comparing the phenotypic and phylogenetic features among this isolate and its related organisms, strain PS10T represents a novel species within the genus Campylobacter, for which the name Campylobacter gastrosuis sp. nov. (Type strain PS10T = GDMCC 1.3686T = JCM 35849T) is proposed.

Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola

Klebsiella variicola, an emerging human pathogen, poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver of the emergence of multiple antibiotic-resistant K. variicola. Clustered regularly interspersed short palindromic repeats (CRISPR) coupled with CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, and can provide acquired immunity against HGT. However, the information about the CRISPR/Cas system in K. variicola is still limited. In this study, 487 genomes of K. variicola obtained from the National Center for Biotechnology Information database were used to analyze the characteristics of CRISPR/Cas systems. Approximately 21.56% of genomes (105/487) harbor at least one confirmed CRISPR array. Three types of CRISPR/Cas systems, namely the type I-E, I-E*, and IV-A systems, were identified among 105 strains. Spacer origin analysis further revealed that approximately one-third of spacers significantly match plasmids or phages, which demonstrates the implication of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tend to target mobile genetic elements from K. pneumoniae. This finding provides new evidence of the interaction of K. variicola and K. pneumoniae during their evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.

Metavirome Analysis and Identification of Midge-Borne Viruses from Yunnan Province, China, in 2021

Midges are widely distributed globally and can transmit various human and animal diseases through blood-sucking. As part of this study, 259,300 midges were collected from four districts in Yunnan province, China, to detect the viral richness and diversity using metavirome analysis techniques. As many as 26 virus families were detected, and the partial sequences of bluetongue virus (BTV), dengue virus (DENV), and Getah virus (GETV) were identified by phylogenetic analysis and PCR amplification. Two BTV gene fragments, 866 bps for the VP2 gene of BTV type 16 and 655 bps for the VP5 gene of BTV type 21, were amplified. The nucleotide sequence identities of the two amplified BTV fragments were 94.46% and 98.81%, respectively, with two classical BTV-16 (GenBank: JN671907) and BTV-21 strains (GenBank: MK250961) isolated in Yunnan province. Furthermore, the BTV-16 DH2021 strain was successfully isolated in C6/36 cells, and the peak value of the copy number reached 3.13 × 107 copies/μL after five consecutive BHK-21 cell passages. Moreover, two 2054 bps fragments including the E gene of DENV genotype Asia II were amplified and shared the highest identity with the DENV strain isolated in New Guinea in 1944. A length of 656 bps GETV gene sequence encoded the partial capsid protein, and it shared the highest identity of 99.68% with the GETV isolated from Shandong province, China, in 2017. Overall, this study emphasizes the importance of implementing prevention and control strategies for viral diseases transmitted by midges in China.

The complete chloroplast genome of Malvaviscus penduliflorus (Malvaceae)

In this study, we assembled the complete chloroplast (cp) genome of Malvaviscus penduliflorus using high-throughput Illumina sequencing reads. The resulting plastome assembly displayed a typical quadripartite structure with a total length of 160,332 bp, containing a pair of inverted repeat regions (IRs) of 26,313 bp separated by a large single-copy region (LSC) of 88,750 bp and a small single-copy region (SSC) of 18,956 bp. The M. penduliflorus cp genome contained 128 genes, and its overall GC content was 36.96%. Phylogenetic analysis among M. penduliflorus and five other Malvaceae species demonstrated that M. penduliflorus was closely related to Urena procumbens and Hibiscus cannabinus. The M. penduliflorus cp genome presented in this study will lay a good foundation for further genetic and genomic studies of the genus Malvaviscus as well as Malvaceae.

Redefining the Genus Corollospora Based on Morphological and Phylogenetic Approaches

The present study, initially to resolve the cryptic species within Corollospora maritima, is to determine how to attain taxonomic discrimination at species and generic levels. Multiple sequence alignments (MSAs) of the ITS, 28S, and 18S regions of the nuclear ribosomal cistron were separately subjected to pairwise distance assessments, Bayesian, and Maximum likelihood phylogenetic analyses. Morphological descriptions of 15 type strains of Corollospora species, along with MSAs involving representatives of the whole genus Corollospora (268 isolates, many from C. maritima sensu lato) totaling 355 published sequences, allowed phylogenetic assessments conducted to the following p-distance thresholds in the ITS/28S regions: ≥3%/1% for species segregation and ≥8%/2% for generic segregation. This resulted in the introduction of 10 new genera encompassing 13 new combinations of current Corollospora species: Ajigaurospora pseudopulchella, Corollosporella anglusa, Corollosporella ramulosa, Corollosporopsis portsaidica, Garethelia parvula, Honshuriella fusca, Keraliethelia pulcehlla, Nakagariella filiformis, Paracorollospora angusta, Paracorollospora luteola, Paracorollospora marina, Shirahamella gracilis, and Tokuratelia colossa. Furthermore, seven undefined genera considered putative new genera (pNGenus A to G), and 16 undefined putative new species (seven spp. come from the resolution of the C. maritima complex), await re-assessment of their morphology and additional molecular data, which may result in the recognition of new taxa.

The complete mitochondrial genome of the Anas platyrhynchos Linnaeus, 1758 breed Longshengcui and its phylogenetic analyses

Duck breed Longshengcui (Anas platyrhynchos Linnaeus, 1758 breed Longshengcui, LSC) is one of the famous native breed of the Guangxi Zhuang Nationality Autonomous Region in China. In this study, we report the complete mitochondrial genome of LSC. The mitogenome (GenBank accession no. MZ895120) has 16,602 bp in length and consisted of the well-known 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and the control region. The phylogenetic analysis showed that LSC and Zhijiang duck have highly similar genetic relationship. These results are helpful for the conservation of genetic resources and phylogeny of this species.

Genetic Diversity of Newcastle Disease Virus Involved in the 2021 Outbreaks in Backyard Poultry Farms in Tanzania

Newcastle disease virus is a significant avian pathogen with the potential to decimate poultry populations all over the world and cause enormous economic losses. Distinct NDV genotypes are currently causing outbreaks worldwide. Due to the high genetic diversity of NDV, virulent strains that may result in a lack of vaccine protection are more likely to emerge and ultimately cause larger epidemics with massive economic losses. Thus, a more comprehensive understanding of the circulating NDV genotypes is critical to reduce Newcastle disease (ND) burden. In this study, NDV strains were isolated and characterized from backyard poultry farms from Tanzania, East Africa in 2021. Reverse-transcription polymerase chain reaction (RT-PCR) based on fusion (F) gene amplification was conducted on 79 cloacal or tracheal swabs collected from chickens during a suspected ND outbreak. Our results revealed that 50 samples out 79 (50/79; 63.3%) were NDV-positive. Sequencing and phylogenetic analyses of the selected NDV isolates showed that 39 isolates belonged to subgenotype VII.2 and only one isolate belonged to subgenotype XIII.1.1. Nucleotide sequences of the NDV F genes from Tanzania were closely related to recent NDV isolates circulating in southern Africa, suggesting that subgenotype VII.2 is the predominant subgenotype throughout Tanzania and southern Africa. Our data confirm the circulation of two NDV subgenotypes in Tanzania, providing important information to design genotype-matched vaccines and to aid ND surveillance. Furthermore, these results highlight the possibility of the spread and emergence of new NDV subgenotypes with the potential of causing future ND epizootics.

Isolation, identification, and pathogenicity of a NADC30-like porcine reproductive and respiratory disorder syndrome virus strain affecting sow production

Since it was first reported in 1987, porcine reproductive and respiratory syndrome virus (PRRSV) has caused several economic crises worldwide. The current prevalence of PRRSV NADC30-like stains causing clinical disease outbreaks in Chain is highly concerning. Immunization against and the prevention of this infection are burdensome for farming organizations as the pathogen frequently mutates and undergoes recombination. Herein, the genetic characterization of a NADC30-like strain (termed BL2019) isolated from a farm in Guangdong Province, China, was analyzed and its pathogenicity for piglets and sows was assessed. Results revealed that BL2019 exhibits a nucleotide homology of 93.7% with NADC30 PRRSV and its NSP2 coding region demonstrates the same 131aa deletion pattern as that of NADC30 and NADC30-like. Furthermore, we identified two recombination breakpoints located nt5804 of the NSP5-coding region and nt6478 of NSP2-coding region, the gene fragment between the two breakpoints showed higher homology to the TJ strain(a representative strain of highly pathogenic PRRSV) compared to the NADC30 strain. In addition, BL2019 infection in piglets caused fever lasting for 1 week, moderate respiratory clinical signs and obvious visual and microscopic lung lesions; infection in gestating sows affected their feed intake and increased body temperature, abortion rates, number of weak fetuses, and other undesirable phenomena. Therefore, we report a NADC30-like PRRSV strain with partial recombination and a representative strain of HP-PRRSV, strain TJ, that can provide early warning and support for PRRS immune prevention and control.

The phylogeny and taxonomy of Glypholecia (Acarosporaceae, lichenized Ascomycota), including a new species from northwestern China

Glypholeciaqinghaiensis An C. Yin, Q. Y. Zhong & Li S. Wang is described as new to science. It is characterized by its squamulose thallus, compound apothecia, ellipsoid ascospores, and the presence of rhizines on the lower surface of the thallus. A phylogenetic tree of Glypholecia species was constructed based on nrITS and mtSSU sequences. Two species G.qinghaiensis and G.scabra are confirmed in China.

Molecular Phylogeny and Morphology Reveal Cryptic Species in the Cordyceps militaris Complex from Vietnam

The Cordyceps militaris complex, which is a special group in the genus Cordyceps, is rich in species diversity and is widely distributed in nature. Throughout the investigations of arthropod-pathogenic fungi in the national reserves and in Vietnam parks, collections of C. militaris attacking lepidopteran pupae or larvae were located in the soil and on the leaf litter. The phylogenetic analyses of the combined nrSSU, nrLSU, TEF, RPB1, and RPB2 sequence data indicated that the fungal materials collected in Vietnam belonged to C. militaris and two hidden species in the C. militaris complex. The phylogenetic analyses and morphological comparisons presented here strongly supported the descriptions of C. polystromata and C. sapaensis as new taxa as well as C. militaris as a known species. The morphological characteristics of 11 species in the C. militaris complex, which included two novel species and nine known taxa, were also compared.

Molecular characterization of Streptococcus agalactiae and Streptococcus dysgalactiae causing bovine mastitis in the southern region of Bangladesh

Objective

This study was conducted to validate polymerase chain reaction (PCR) as a confirmatory diagnostic tool to find out the presence and frequency of Streptococcus agalactiae (S. agalactiae) and Streptococcus dysgalactiae (S. dysgalactiae) in mastitic milk samples obtained from dairy cows in the southern region of Bangladesh.

Materials and Methods

A total of 196 samples of bovine milk were collected from various dairy farms in the Chattogram metropolitan area of the southern part of Bangladesh. DNA extracted from isolates obtained by culturing California mastitis test (CMT)-positive mastitic milk samples (n = 146) on 5% sheep blood agar was used as a template for PCR. Two sets of specific primers based on the 16S rRNA gene were used to discriminate between S. agalactiae and S. dysgalactiae. Four PCR products were subjected to sequencing, followed by phylogenetic analysis.

Results

The PCR analyses revealed that out of the 146 CMT-positive milk samples tested, 29 samples were positive for S. agalactiae (19.86%), while 26 samples were positive for S. dysgalactiae (17.81%). Further sequence analysis of the corresponding PCR products and bioinformatics analysis verified the results.

Conclusion

The study proves the efficiency of PCR as a useful diagnostic approach to determine the presence and prevalence of S. agalactiae and S. dysgalactiae in mastitic milk samples obtained from dairy cows.

Morphological and molecular analyses reveal two new species of Microcera (Nectriaceae, Hypocreales) associated with scale insects on walnut in China

The fungal genus Microcera consists of species mostly occurring as parasites of scale insects, but are also commonly isolated from soil or lichens. In the present study, we surveyed the diversity and assess the taxonomy of entomopathogenic fungi in Sichuan Province, China. Two new species of Microcera, viz. M.chrysomphaludis and M.pseudaulacaspidis, were isolated from scale insects colonising walnut (Juglansregia). Maximum Likelihood and Bayesian Inference analyses of ITS, LSU, tef1-α, rpb1, rpb2, acl1, act, tub2, cmdA and his3 sequence data provide evidence for the validity of the two species and their placement in Nectriaceae (Hypocreales). Microcerapseudaulacaspidis primarily differs from similar species by having more septate and smaller cylindrical macroconidia, as well as DNA sequence data. Meanwhile, Microcerachrysomphaludis has elliptical, one-septate ascospores with acute ends and cylindrical, slightly curved with 4-6 septate macroconidia up to 78 µm long. Morphological descriptions with illustrations of the novel species and DNA-based phylogeny generated from analyses of multigene dataset are also provided to better understand species relationships.

Simplicillium sinense sp. nov., a novel potential pathogen of tinea faciei

Simplicillium species are widely distributed with a broad spectrum of hosts and substrates. Generally, these species are entomopathogenic or mycoparasitic. Notably, some isolates of Simplicillium lanosoniveum and Simplicillium obclavatum were obtained from human tissues. In this study, two fungi were isolated from the annular itchy patch of infected skin of a 46-year-old man with diabetes mellitus. Based on a combination of morphological characteristics and phylogenetic analysis, a novel species, Simplicillium sinense, was introduced herein. It morphologically differs from the remaining Simplicillium in the size of phialides and conidia. Additionally, it grows slowly on YPD at 37°C. Antimicrobial susceptibility testing presented that this fungus is resistant to most azole antifungals. Therefore, the diagnosis of tinea faciei was made, and after 2 weeks of being treated with oral terbinafine (250 mg, once a day) and topical terbinafine cream for 1 month, the rash was mainly resolved and no recurrence happened after 6 months of follow-up. Herein, Simplicillium sinense was introduced as a new fungal taxon. Meanwhile, a case of superficial infection caused by S. sinense was reported. So far, it is the third Simplicillium species obtained from human tissue. Meanwhile, terbinafine is recommended as the first-line antifungal treatment against Simplicillium infection.

Isolation and Genomic Characteristics of Cat-Borne Campylobacter felis sp. nov. and Sheep-Borne Campylobacter ovis sp. nov

Nine novel bacterial strains were isolated from the feces of cats and sheep in 2019 and 2020 in Beijing, China. Cells were 1-3 μm long and ≤0.5 μm wide, Gram-stain negative, microaerobic, motile, oxidase positive, and urease negative. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these nine isolates belong to the genus Campylobacter but formed two robust clades that were clearly separate from the currently recognized species and, respectively, isolated from the cat and sheep. Both these strains shared low 16S rRNA gene sequence similarity, dDDH relatedness, and ANI values with their closest species C. upsaliensis CCUG 14913^T and C. lanienae NCTC 13004^T, and against each other, which are below the cut-off values generally recognized for isolates of the same species. The genomic DNA G + C contents of type strains XJK22-1^T and SYS25-1^T were 34.99 mol% and 32.43 mol%, respectively. Electron microscopy showed that these cells were spiral shaped, with bipolar single flagella. Based on results from genotypic, phenotypic, phylogenetic, and phylogenomic analyses, these nine strains represent two novel species within the genus Campylobacter, for which the names Campylobacter felis sp. nov. (Type strain XJK22-1^T = GDMCC 1.3684^T = JCM 35847^T) and Campylobacter ovis sp. nov. (Type strain SYS25-1^T = GDMCC 1.3685^T) are proposed.

Global Analyses of Multi-Locus Sequence Typing Data Reveal Geographic Differentiation, Hybridization, and Recombination in the Cryptococcus gattii Species Complex

Cryptococcus gattii species complex (CGSC) is a basidiomycete haploid yeast and globally distributed mammalian pathogen. CGSC is comprised of six distinct lineages (VGI, VGII, VGIII, VGIV, VGV, and VGVI); however, the geographical distribution and population structure of these lineages is incompletely described. In this study, we analyze published multi-locus sequence data at seven loci for 566 previously recorded sequence types (STs) encompassing four distinct lineages (VGI, VGII, VGIII, and VGIV) within the CGSC. We investigate indicators of both clonal dispersal and recombination. Population genetic analyses of the 375 STs representing 1202 isolates with geographic information and 188 STs representing 788 isolates with ecological source data suggested historically differentiated geographic populations with infrequent long-distance gene flow. Phylogenetic analyses of sequences at the individual locus and of the concatenated sequences at all seven loci among all 566 STs revealed distinct clusters largely congruent with four major distinct lineages. However, 23 of the 566 STs (4%) each contained alleles at the seven loci belonging to two or more lineages, consistent with their hybrid origins among lineages. Within each of the four major lineages, phylogenetic incompatibility analyses revealed evidence for recombination. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across all samples. Together, our results suggest evidence for historical geographical differentiation, sexual recombination, hybridization, and both long-distance and localized clonal expansion in the global CGSC population.

The Complete Mitochondrial Genome of the Hermit Crab Diogenes edwardsii (Anomura: Diogenidae) and Phylogenetic Relationships within Infraorder Anomura

A complete mitochondrial genome (mitogenome) can provide important information for gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few mitogenomes of hermit crabs (superfamily Paguridae) in the infraorder Anomura have been reported. This study reports the first complete mitogenome of the hermit crab Diogenes edwardsii assembled using high-throughput sequencing. The mitogenome of Diogenes edwardsii is 19,858 bp in length and comprises 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. There are 28 and six genes observed on the heavy and light strands, respectively. The genome composition was highly A + T biased (72.16%), and exhibited a negative AT-skew (-0.110) and positive GC-skew (0.233). Phylogenetic analyses based on the nucleotide dataset of 16 Anomura species indicated that D. edwardsii was closest related to Clibanarius infraspinatus in the same family, Diogenidae. Positive selection analysis showed that two residues located in cox1 and cox2 were identified as positively selected sites with high BEB value (>95%), indicating that these two genes are under positive selection pressure. This is the first complete mitogenome of the genus Diogenes, and this finding helps us to represent a new genomic resource for hermit crab species and provide data for further evolutionary status of Diogenidae in Anomura.

Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae)

Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I-IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC-petN, trnL-rpl32, ndhD-ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences

The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies-Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae-which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies-Crocoideae, Nivenioideae, and Aristeoideae-shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.

New Insights into the Origin and Evolution of Mysmenid Spiders (Araneae, Mysmenidae) Based on the First Four Complete Mitochondrial Genomes

The mitochondrial genome (mitogenome) is recognized as an effective molecular marker for studying molecular evolution and phylogeny. The family Mysmenidae is a group of widely distributed and covert-living spiders, of which the mitogenomic information is largely unclear. In this study, we obtained the first four complete mitogenomes of mysmenid spiders (one aboveground species: Trogloneta yuensis, and three cave-dwelling species: T. yunnanense, Yamaneta kehen and Y. paquini). Comparative analyses revealed that their lengths ranged from 13,771 bp (T. yuensis) to 14,223 bp (Y. kehen), containing a standard set of 37 genes and an A + T-rich region with the same gene orientation as other spider species. The mitogenomic size of T. yunnanense was more similar to that of Yamaneta mitogenomes than that of T. yuensis, which might indicate the convergent evolution of cave spiders. High variability was detected between the genera Trogloneta and Yamaneta. The A + T content, the amino acid frequency of protein-coding genes (PCGs) and the secondary structures of tRNAs showed large differences. Yamaneta kehen and Y. paquini contained almost identical truncated tRNAs, and their intergenic spacers and overlaps exhibited high uniformity. The two Yamaneta species also possessed a higher similarity of start/stop codons for PCGs than the two Trogloneta species. In selective pressure analysis, compared to Yamaneta, Trogloneta had much higher Ka/Ks values, which implies that selection pressure may be affected by habitat changes. In our study, the phylogenetic analysis based on the combination of 13 PCGs and two rRNAs showed that Mysmenidae is a sister clade to the family Tetragnathidae. Our data and findings will contribute to the better understanding of the origin and evolution of mysmenid spiders.

Characterization of the complete plastid genome of Korean endemic, Ajuga spectabilis Nakai (Lamiaceae)

Ajuga spectabilis Nakai is a Korean endemic species in Lamiaceae. In spite of its importance, genomic studies are not performed on this species. Here, we report the complete plastid genome sequences of A. spectabilis, which will provide valuable information for its natural conservation and future studies for the plastid genome evolution. The plastid genome is 150,417 bp in length, containing a large single-copy region (LSC) of 82,140 bp and a small single-copy (SSC) region of 17,165 bp which are separated by a pair of inverted repeats (IR) of 25,556 bp. It encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content is 38.3%, and those in the LSC, SSC, and IR regions are 36.4%, 32.2%, and 43.3%, respectively, which is consistent with other Ajuga species. Our phylogenetic analysis revealed that A. spectabilis formed a close relationship with A. ciliata and A. decumbens.

Morphology and Phylogeny of Lyophylloid Mushrooms in China with Description of Four New Species

The lyophylloid agarics are a group of ecologically highly diversified macrofungi, some of which are very popular edible mushrooms. However, we know little about lyophylloid species diversity in China. In this study, we described four new species from China: Lyophyllum atrofuscum, L. subalpinarum, L. subdecastes, and Ossicaulis sichuanensis. We conducted molecular phylogenetic analyses of Lyophyllaceae based on the nuclear ribosomal RNA gene (nLSU) and the internal transcribed spacer regions (ITS). Phylogenetic analyses by the maximum likelihood method and Bayesian inference showed that the four new species are unique monophyletic species. A key to the species of Lyophyllum from China and a key to Ossicaulis worldwide were given.

Genome-Wide Identification, Characterization, and Expression Analysis of GRAS Gene Family in Ginger (Zingiber officinale Roscoe)

GRAS family proteins are one of the most abundant transcription factors in plants; they play crucial roles in plant development, metabolism, and biotic- and abiotic-stress responses. The GRAS family has been identified and functionally characterized in some plant species. However, this family in ginger (Zingiber officinale Roscoe), a medicinal crop and non-prescription drug, remains unknown to date. In the present study, 66 GRAS genes were identified by searching the complete genome sequence of ginger. The GRAS family is divided into nine subfamilies based on the phylogenetic analyses. The GRAS genes are distributed unevenly across 11 chromosomes. By analyzing the gene structure and motif distribution of GRAS members in ginger, we found that the GRAS genes have more than one cis-acting element. Chromosomal location and duplication analysis indicated that whole-genome duplication, tandem duplication, and segmental duplication may be responsible for the expansion of the GRAS family in ginger. The expression levels of GRAS family genes are different in ginger roots and stems, indicating that these genes may have an impact on ginger development. In addition, the GRAS genes in ginger showed extensive expression patterns under different abiotic stresses, suggesting that they may play important roles in the stress response. Our study provides a comprehensive analysis of GRAS members in ginger for the first time, which will help to better explore the function of GRAS genes in the regulation of tissue development and response to stress in ginger.

Morphology, phylogeny, mitogenomics and metagenomics reveal a new entomopathogenic fungus Ophiocordycepsnujiangensis (Hypocreales, Ophiocordycipitaceae) from Southwestern China

Ophiocordyceps contains the largest number of Cordyceps sensu lato, various species of which are of great medicinal value. In this study, a new entomopathogenic fungus, Ophiocordycepsnujiangensis, from Yunnan in southwestern China, was described using morphological, phylogenetic, and mitogenomic evidence, and its fungal community composition was identified. It was morphologically characterized by a solitary, woody, and dark brown stromata, smooth-walled and septate hyphae, solitary and gradually tapering conidiogenous cells with plenty of warty protrusions, and oval or fusiform conidia (6.4-11.2 × 3.7-6.4 µm) with mucinous sheath. The phylogenetic location of O.nujiangensis was determined based on the Bayesian inference (BI) and the maximum likelihood (ML) analyses by concatenating nrSSU, nrLSU, tef-1a, rpb1, and rpb2 datasets, and ten mitochondrial protein-coding genes (PCGs) datasets (atp6, atp9, cob, cox2, nad1, nad2, nad3, nad4, nad4L, and nad5). Phylogenetic analyses revealed that O.nujiangensis belonged to the Hirsutellasinensis subclade within the Hirsutella clade of Ophiocordyceps. And O.nujiangensis was phylogenetically clustered with O.karstii, O.liangshanensis, and O.sinensis. Simultaneously, five fungal phyla and 151 fungal genera were recognized in the analysis of the fungal community of O.nujiangensis. The fungal community composition differed from that of O.sinensis, and differences in the microbial community composition of closely related species might be appropriate as further evidence for taxonomy.

Globisporangium coniferarum sp. nov., associated with conifers and Quercus spp

During a survey of gardens in Shiraz County, Iran, aimed at identifying oomycetes associated with roots of ornamental trees, a species of Globisporangium with distinctive morphological characters separating it from other known species in this genus was recovered from conifers and occasionally from a Quercus sp. Five isolates of this species were characterised. Phylogenetic analyses of nuclear (ITS and βtub) and mitochondrial (cox1 and cox2) loci using Bayesian inference and maximum likelihood analyses as well as their distinct morphological and cultural characteristics (e.g., abundant production of chlamydospores; globose, ellipsoid to ovoid sporangia; amorphous oogonia with a smooth wall; paragynous to rarely hypogynous antheridia and 1-5 antheridia per oogonium; mostly plerotic oospores) revealed that these isolates belong to a new Globisporangium species grouping in the phylogenetic clade G of Pythium sensu lato. This paper formally describes Globisporangium coniferarum sp. nov. as a new species and compares it with other phylogenetically related and already known Globisporangium species, including G. nagaii, G. violae, G. paddicum, G. okanoganense, G. iwayamae and G. canariense. Citation: Salmaninezhad F, Aloi F, Pane A, Mostowfizadeh-Ghalamfarsa R, Cacciola SO (2022). Globisporangium coniferarum sp. nov., associated with conifers and Quercus spp. Fungal Systematics and Evolution 10: 127-137. doi: 10.3114/fuse.2022.10.05.

Hanseniatrifoliolata, a new species (Apiaceae) from Shaanxi, China

Hanseniatrifoliolata Q.P.Jiang & X.J.He (Apiaceae), is described as new from Shaanxi Province, northwest China. The mericarp features of H.trifoliolata resemble H.himalayensis and H.phaea and molecular phylogenetic analyses (combining ITS and plastid genomes data) suggest that H.trifoliolata is closely related to the group formed by H.oviformis and H.forbesii. The new species H.trifoliolata has unique 3-foliolate leaves and differ from other Hansenia species in its leaves, umbel numbers and size. A comprehensive description of H.trifoliolata is provided, including habitat environment and detailed morphological traits.

Phylogeny and Systematics of the Genus Tolypocladium (Ophiocordycipitaceae, Hypocreales)

The taxonomy and phylogeny of the genus Tolypocladium are herein revised based on the most comprehensive dataset to date. Two species-level phylogenies of Tolypocladium were constructed: a single-gene phylogeny (ITS) of 35 accepted species and a multigene phylogeny (nrSSU, nrLSU, tef-1α, rpb1, and rpb2) of 27 accepted species. Three new species, Tolypocladium pseudoalbum sp. nov., Tolypocladium subparadoxum sp. nov., and Tolypocladium yunnanense sp. nov., are described in the present study. The genetic divergences of four markers (ITS, tef-1α, rpb1 and rpb2) among Tolypocladium species are also reported. The results indicated that species of Tolypocladium were best delimited by rpb1 sequence data, followed by the sequence data for the rpb2, tef-1α, and ITS provided regions. Finally, a key to the 48 accepted species of Tolypocladium worldwide is provided.

A Novel Mitochondrial Genome Fragmentation Pattern in the Buffalo Louse Haematopinus tuberculatus (Psocodea: Haematopinidae)

Sucking lice are obligate ectoparasites of mammalian hosts, causing serious public health problems and economic losses worldwide. It is well known that sucking lice have fragmented mitochondrial (mt) genomes, but many remain undetermined. To better understand patterns of mt genome fragmentation in the sucking lice, we sequenced the mt genome of the buffalo louse Haematopinus tuberculatus using next-generation sequencing (NGS). The mt genome of H. tuberculatus has ten circular minichromosomes containing a total of 37 genes. Each minichromosome is 2.9-5.0 kb long and carries one to eight genes plus one large non-coding region. The number of mt minichromosomes of H. tuberculatus (ten) is different from those of congeneric species (horse louse H. asini, domestic pig louse H. suis and wild pig louse H. apri) and other sucking lice. Two events (gene translocation and merger of mt minichromosome) are observed in Haematopinus. Compared to other studies, our phylogeny generated from mt genome datasets showed a different topology, suggesting that inclusion of data other than mt genomes would be required to resolve phylogeny of sucking lice. To our knowledge, this is the first report of a ten mt minichromosomes genome in sucking lice, which opens a new outlook into unexplored mt genome fragmentation patterns in sucking lice.

Characterization of the complete chloroplast genome sequence of Elaeagnus henryi Warb. ex Diels (Elaeagnaceae)

Elaeagnus henryi Warb. ex Diels belongs to the Elaeagnaceae. Here, we reveal the complete chloroplast genome of Elaeagnus henryi. The complete chloroplast genome is 152,244 bp in length and contains a large single-copy (LSC) region of 82,235 bp, a small single-copy (SSC) region of 18,279 bp and a pair of inverted repeats (IRs) of 25,865 bp. There are 126 genes, including 81 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. The total GC content of the chloroplast genome sequence is 37.1%. The maximum-likelihood phylogenetic analysis indicated that E. henryi was sister to Elaeagnus pungens (MW145133). The result may be because the species are advanced and developed from the same ancestor.

Genome-wide characterization and evolutionary analysis of linker histones in castor bean (Ricinus communis)

H1s, or linker histones, are ubiquitous proteins in eukaryotic cells, consisting of a globular GH1 domain flanked by two unstructured tails. Whilst it is known that numerous non-allelic variants exist within the same species, the degree of interspecific and intraspecific variation and divergence of linker histones remain unknown. The conserved basic binding sites in GH1 and evenly distributed strong positive charges on the C-terminal domain (CTD) are key structural characters for linker histones to bind chromatin. Based on these features, we identified five linker histones from 13 GH1-containing proteins in castor bean (Ricinus communis), which were named as RcH1.1, RcH1.2a, RcH1.2b, RcH1.3, and RcH1.4 based on their phylogenetic relationships with the H1s from five other economically important Euphorbiaceae species (Hevea brasiliensis Jatropha curcas, Manihot esculenta Mercurialis annua, and Vernicia fordii) and Arabidopsis thaliana. The expression profiles of RcH1 genes in a variety of tissues and stresses were determined from RNA-seq data. We found three RcH1 genes (RcH1.1, RcH1.2a, and RcH1.3) were broadly expressed in all tissues, suggesting a conserved role in stabilizing and organizing the nuclear DNA. RcH1.2a and RcH1.4 was preferentially expressed in floral tissues, indicating potential involvement in floral development in castor bean. Lack of non-coding region and no expression detected in any tissue tested suggest that RcH1.2b is a pseudogene. RcH1.3 was salt stress inducible, but not induced by cold, heat and drought in our investigation. Structural comparison confirmed that GH1 domain was highly evolutionarily conserved and revealed that N- and C-terminal domains of linker histones are divergent between variants, but highly conserved between species for a given variant. Although the number of H1 genes varies between species, the number of H1 variants is relatively conserved in more closely related species (such as within the same family). Through comparison of nucleotide diversity of linker histone genes and oil-related genes, we found similar mutation rate of these two groups of genes. Using Tajima's D and ML-HKA tests, we found RcH1.1 and RcH1.3 may be under balancing selection.

Characterization and Pathogenicity of Two Novel PRRSVs Recombined by NADC30-like and NADC34-like Strains in China

Porcine reproductive and respiratory syndrome viruses (PRRSVs) pose a serious threat to the swine industry in China, which has caused great difficulties for porcine reproductive and respiratory syndrome (PRRS) immune prevention and control, due to its easily mutable and recombinant nature. In this study, two novel PRRSV strains, which were named GD-H1 and GD-F1, were isolated and fully sequenced from pig farms in Guangdong province, China. The phylogenetic analysis and recombination analysis revealed that the GD-H1 and GD-F1 were generated by the recombination of NADC30-like and NADC34-like strains which were different from the previously prevalent strain. Further pathogenic studies on piglets and sows found that the recombinant strains could cause piglets high fever, loss of appetite and lung lesions, but no piglets died. However, the recombinant strains could cause acute death and abortion in pregnant sow infection models together with average survival rates of 62.5% and 37.5% abortion rates, respectively. These findings indicated that the recombinant strains were extremely pathogenic to sows. Therefore, we report two clinical novel recombinant strains of PRRSV that are different from the traditional epidemic strains in China, which may provide early warning and support for PRRS immune prevention and control.