High Bootstrap Values Research Articles

Complete chloroplast genome and phylogenetic analysis of Amorphophallus paeoniifolius (Araceae)

Amorphophallus paeoniifolius (Dennst.) Nicolson, 1885, often known as elephant foot yam, is a tropical tuber crop that originates from south-east Asia and belongs to the Araceae family. It is known for its high production potential and popularity as a medicinal plant. However, the phylogeny and genes for this species are still unavailable. In this study, the first complete chloroplast genome of A. paeoniifolius was reported and phylogenetic analysis was conducted with Araceae species. The chloroplast genome was 176,258 bp in length with 34.80% overall GC content and includes a large single-copy (LSC) region (93,951 bp), a small single-copy (SSC) region (15,013 bp), and a pair of inverted repeat (IRs) regions (33,647 bp). The chloroplast genome has 130 genes, which include 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A maximum-likelihood (ML) phylogenetic analysis indicated that all Amorphophallus species formed a single monophyletic clade with a high bootstrap value and A. paeoniifolius was closely related to A. konjac, A. albus, A. krausei, and A. titanum. The chloroplast genome reported in this study will be useful for further taxonomic and evolutionary studies of Amorphophallus.

A New Species of Hydrozoan Jellyfish Eutima onahamaensis and New Record of Eutima diademata (Hydrozoa, Leptothecata) from Japan

The family Eirenidae is one of the major taxa of the order Leptothecata, comprising approximately 80 species from ten genera. In this study, taxonomic investigations, including morphological observations and molecular 16S phylogenetic analyses, were conducted on unknown Eirenidae specimens collected off the coast of Iwaki, Fukushima Prefecture, eastern Japan, in June 2022. The specimens had the following morphological characteristics: marginal warts and tentacular bulbs with lateral cirri and without adaxial papillae, a mouth with simple lips, four simple radial canals, and eight statocysts common to the genus Eutima. However, this species can be distinguished from other species of Eutima by the number of tentacles, number and shape of marginal warts, position of the gonads, and gastric peduncle length. Moreover, the monophyly of the species was evident in the 16S rRNA phylogenetic tree (as indicated by the high bootstrap value of 100%), thereby supporting the validity of the new species. Based on these results, we describe it as a new species, Eutima onahamaensis, for taxonomic stabilization. We also made detailed observations of the morphology and molecular phylogenetic analyses of one of the species newly recorded in Japan: Eutima diademata. A comparative table of the primary diagnostic characteristics of Eutima has been provided. This study provided taxonomic keys for identifying species in the genus Eutima.

Volatile Profiles and DNA Barcodes of Myrtaceae Species with Occurrence in the Brazilian Amazon.

Myrtaceae family includes many species with taxonomic challenges, making it one of the most complex families to identify. This study used DNA barcoding to find molecular markers for species authentication based on the Myrtaceae family's chemical composition and genetic diversity. Essential oils and genetic material were extracted from the leaves of six different species: Eugenia uniflora, E. patrisii, Myrcia splendens, Psidium guajava, P. guineense, and Psidium sp. The samples were analyzed based on compound classes and grouped into two categories. Group I included samples with high amounts of oxygenated sesquiterpenes (3.69-76.05 %) and fatty acid derivatives (0.04-43.59 %), such as E. uniflora, Myrcia splendens, and E. patrisii. Group II included samples P. guajava, P. guineense, and Psidium sp., which had a significant content of monoterpene hydrocarbons (0.69-72.35 %), oxygenated sesquiterpenes (8.06-68.1 %), phenylpropanoids (0.45-22.59 %), and sesquiterpene hydrocarbons (0.27-21.84 %). The PsbA-trnH gene sequences had a high genetic variability, allowing the species to be distinguished. A phylogenetic analysis showed two main clusters with high Bootstrap values corresponding to the subtribes Eugeniineae, Myrciinae, and Pimentinae. The results suggest a weak correlation between genetic and chemical data in these Myrtaceae species.

Roseinatronobacter alkalisoli sp. nov., an alkaliphilic bacterium isolated from soda soil, and genome-based reclassification of the genera Rhodobaca and Roseinatronobacter.

The genera Rhodobaca and Roseinatronobacter are phylogenetically related genera within the family Paracoccaceae. Species of these genera were described using 16S rRNA gene-based phylogeny and phenotypic characteristics. However, the 16S rRNA gene identity and phylogeny reveal the controversy of the taxonomic status of these two genera. In this work, we examined the taxonomic positions of members of both genera using 16S rRNA gene phylogeny, phylogenomic analysis and further validated using overall genome-related indexes, including digital DNA-DNA hybridization, average nucleotide identity, average amino acid identity and percentage of conserved proteins. Based on phylogenetic and phylogenomic results, the current four species of the two genera clustered tightly into one clade with high bootstrap values, suggesting that the genus Rhodobaca should be merged with Roseinatronobacter. In addition, a novel species isolated from a soda soil sample collected from Anda City, PR China, and designated as HJB301T was also described. Phenotypic, chemotaxonomic, genomic and phylogenetic properties suggested that strain HJB301T (=CCTCC AB 2021113T=KCTC 82977T) represents a novel species of the genus Roseinatronobacter, for which the name Roseinatronobacter alkalisoli sp. nov. is proposed.

The complete chloroplast genome of Oxytropis ochrocephala Bunge 1874 (Fabaceae) and its phylogenetic analysis

This study presents the first-ever complete chloroplast (cp) genome sequence of Oxytropis ochrocephala Bunge 1874, a member of the Fabaceae family. The cp genome spans 126,996 base pairs and includes 109 genes, comprising 76 protein-coding genes, 29 tRNA genes, and four rRNA genes. Notably, the genome lacks an inverted repeat (IR) region. Additionally, we constructed phylogenetic trees for 34 species within Trib. Galegeae, employing both maximum likelihood (ML) and Bayesian inference (BI) methods. These analyses robustly support the monophyly of the Oxytropis species, evidenced by high bootstrap values (BP = 100) and posterior probabilities (PP = 1). Within this clade, O. ochrocephala exhibits a sister relationship with other Oxytropis species. Our findings provide valuable insights into the genetic makeup and evolutionary relationships of O. ochrocephala within the Galegeae tribe.

Complete mitochondrial DNA sequence of Alboglossiphonia lata Oka, 1910 (Rhynchobdellida: Glossiphoniidae) and its phylogenetic analysis

The complete mitochondrial genome of Alboglossiphonia lata (basionym: Glossiphonia lata), sourced from a biodiversity hotspot of China, has been determined and reported in this study. It was 15,236 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and three control regions. The mitogenome was deposited GenBank under the accession number PP165800. A. lata and other species within the Glossiphoniidae family were clustered together with high bootstrap values. The mitochondrial genome of A. lata provides valuable molecular data for further phylogenetic research on the Glossiphoniidae family.

A new species of trout from the Köprüçay River, a drainage of Mediterranean Sea, Türkiye (Salmoniformes, Salmonidae)

Salmo ekmekciae, new species, is described from the Köprüçay River, a drainage of Mediterranean Sea. It is distinguished from Salmo species in adjacent water by having 9–10 parr marks on flank; 11–13 scale rows between end of base of adipose-fin and lateral line; 22–24 gill rakers on first gill arch; a shorter distance between adipose-fin and caudal-fin base; a slenderer caudal peduncle; and a slenderer body at adipose-fin origin. According to the Bayesian, and maximum likelihood analyses, Salmo ekmekciae cyt b gene resulted in coherent trees supported by high bootstrap values.

The complete chloroplast genome assembly of Castanopsis orthacantha Franch. 1899 (Fagaceae) in Southwestern China

Castanopsis orthacantha Franch. 1899 is one representative tree species distributed in the evergreen broad-leaved forests of southwestern China. This species is an important source of timber for manufacturing furniture, floors, and paper. It also plays a significant role in maintaining ecological balance and stability. To help with the genetic diversity assessment of C. orthacantha, we sequenced and assembled the first complete chloroplast genome. The length of the chloroplast genome was 160,588 bp, with a typical quadripartite structure (GenBank accession no. OR900101). The large single-copy (LSC), small single-copy (SSC), and two inverted repeats (IRs) were 90,237 bp, 18,953 bp, and 25,699 bp in length, respectively. We annotated one hundred and thirty genes across the chloroplast genome, including 86 protein-coding genes (79 are unique), 37 tRNA genes (29 are unique), and eight rRNA genes (four are unique). Seventeen genes had one intron, and four were detected with two introns. The maximum likelihood phylogeny suggested that C. orthacantha, C. lamontii, C. sclerophylla, and C. hainanensis formed a clade with a high bootstrap value. This newly sequenced chloroplast genome assembly will aid in the population genetic and phylogenetic studies of Castanopsis species in the future.

Oriental beech decline caused by Brenneria alni

AbstractHyrcanian forests comprise a long strip along the southern coast of the Caspian Sea in northern Iran. Oriental beech (Fagus orientalis) is one of the most valuable forest tree species in the Hyrcanian forests. Bark necrosis and bleeding spots of oriental beech were observed in Savadkuh forests in Mazandaran province during summer 2021. Ten samples were collected from symptomatic oriental beech trees. The bark canker symptoms included stem tissue necrosis, dark brown to black spots on the trunk, bleeding with dark exudates and dark lesions in the inner bark. Twenty‐six strains of culturable bacteria were isolated from the samples which in culture were predominantly round, convex, smooth with entire margins on nutrient agar and a metallic green sheen pigment on eosin‐methylene blue (EMB) agar. Fourteen strains induced necrosis and browning of the tissues around the inoculation sites on acorns after 2 weeks. Five representative strains also caused dieback in twigs of oriental beech 3 weeks after inoculation. These bacteria were Gram‐negative, catalase positive and oxidase negative. All strains produced colonies with a green metallic sheen on EMB agar. Strains were negative in tests for starch and gelatine hydrolysis or production of levan. A phylogenetic tree based on concatenated sequences of gyrB and infB genes, of representative strains well as in each of the single gene‐based phylogenetic trees, indicated that these strains clustered with Brenneria alni NCPPB 3934T with high bootstrap values. To the best of our knowledge, this is the first report of B. alni associated with bark necrosis and bleeding spots on oriental beech.

Revisiting the genotypes of Theileria equi based on the V4 hypervariable region of the 18S rRNA gene.

Equine theileriosis, an economically important disease that affects horses and other equids worldwide, is caused by a tick-borne intracellular apicomplexan protozoa Theileria equi. Genotyping of T. equi based on the 18S rRNA gene revealed the presence of two, three, four or five genotypes. In previous published reports, these genotypes have been labelled either alphabetically or numerically, and there is no uniformity in naming of these genotypes. The present study was aimed to revisit the phylogeny, genetic diversity and geographical distribution of T. equi based on the nucleotide sequences of the V4 hypervariable region of the 18S rRNA gene available in the nucleotide databases. Out of 14792 nucleotide sequences of T. equi available in the GenBank™, only 736 sequences of T. equi containing the complete V4 hypervariable region of the 18S rRNA gene (>207 bp) were used in multiple sequence alignment. Subsequently, a maximum likelihood phylogenetic tree was constructed based on the Kimura 2-parameter model (K2+I). The phylogenetic tree placed all the sequences into four distinct clades with high bootstrap values which were designated as T. equi clades/ genotypes A, B, C and D. Our results indicated that the genotype B of Nagore et al. and genotype E of Qablan et al. together formed the clade B with a high bootstrap value (95%). Furthermore, all the genotypes probably originated from clade B, which was the most dominant genotype (52.85%) followed by clades A (27.58%), and C (9.78%) and D (9.78%). Genotype C manifested a comparatively higher genetic diversity (91.0-100% identity) followed by genotypes A (93.2-99.5%), and B and D (95.7-100%). The alignment report of the consensus nucleotide sequences of the V4 hypervariable region of the 18S rRNA gene of four T. equi genotypes (A-D) revealed significant variations in one region, between nucleotide positions 113-183, and 41 molecular signatures were recognized. As far as geographical distribution is concerned, genotypes A and C exhibited far-extending geographical distribution involving 31 and 13 countries of the Asian, African, European, North American and South American continents, respectively. On the contrary, the genotypes B and D exemplified limited distribution with confinement to 21 and 12 countries of Asian, African and European continents, respectively. Interestingly, genotypes A and C have been reported from only two continents, viz., North and South America. It was observed that genotypes A and C, and B and D exhibit similar geographical distribution. The present study indicated the presence of only four previously described T. equi genotypes (A, B, C and D) after performing the molecular analyses of all available sequences of the complete V4 hypervariable region of the 18S rRNA gene of T. equi isolates in the GenBank™.

Characterization of the chloroplast genome sequence of Calophyllum inophyllum, a bioenergy tree species, using Oxford Nanopore Technologies

Calophyllum inophyllum is a forest tree species that offers significant renewable energy benefits. However, the genetic information of these bioenergy tree species for the study of tree improvement is still limited. This study aimed to assemble the draft chloroplast genome using MinION Oxford Nanopore Technologies (ONT) and analyze the genetic relationship based on molecular markers for C. inophyllum. The study involved several steps: DNA extraction and isolation using the CTAB method, DNA library preparation, DNA sequencing using MinION Oxford Nanopore Technologies (ONT), and phylogenetic analysis based on selected DNA markers. The results showed that 115.1 Mb of high-quality DNA was successfully generated using ONT long-read sequencing, and 114.708 bp was annotated into partial genome chloroplast. The genetic relationship analysis using two selected DNA barcodes, namely rbcL and accD showed that the accD gene is more recommended for constructing a phylogenetic tree for the genus Calophyllum than the rbcL gene as it has a high bootstrap value (93%). Furthermore, the accD gene can also be considered a potential marker for further genetic analysis of C. inophyllum.

First Report of Anthracnose on Ilex cornuta Caused by Colletotrichum aenigma in China

Ilex cornuta (Aquifoliaceae) is a dark green evergreen shrub with glossy leaves that is widely distributed in China and East Asia and used as an ornamental and medicinal plant. In March 2022, typical symptoms of anthracnose were observed on I. cornuta leaves (with approximately 30% of leaves affected) in Jiangxi Academy of Forestry, Nanchang city, Jiangxi Province, China. The early symptoms were light brown spots on the edge or tip of the leaves. The spots gradually expanded to ovoid-shaped lesions and eventually become necrotic, dry, and gray with a dark brown margins. To isolate the pathogen, ten symptomatic leaves were randomly collected, the edges between diseased area and healthy area were cut into small pieces (4×4 mm), surface sterilized by dipping in 70% ethanol for 30 s and 1% sodium hypochlorite (NaClO) for 30 s, and then washed three times with sterile distilled water. Leaf pieces were then placed on potato dextrose agar (PDA) plates at 28℃ in the dark. Subsequently, six isolates were obtained using the single-spore method, five of them were similar in morphological characteristics. Colonies grown on PDA for 7 days were 75-85 mm in diameter, and were cottony, dense, and pale white on the surface and white to grayish-green on the reverse side. Conidia were single-celled, transparent and subcylindrical to clavate. The contents of the conidia were granular and 15.63–20.63 × 5.63–7.50 μm in size (=17.78 ± 1.41× 6.50 ± 0.55 μm, n = 40). The species was also identified by analysis of the internal transcribed spacer (ITS) region, actin (ACT), glyceradehyde-3-phosphate dehydrogenase (GAPDH) and β-tubulin (TUB2), calmodulin (CAL), glutamine gynthetase (GS), DNA Lyase (APN2), intergenic spacer and partial mating type (ApMat) genes using ITS4/ITS5, ACT-512F/ACT-783R, GDF/GDR, T1/Bt2b, CL1C/CL2C, GSF/GSR, ColDL-F3/CgDL-R1 and CgDL-F6/CgMAT1F2 primers, respectively (Weir, et al. 2012; Maharachchikumbura, et al. 2014; Khodadadi, et al. 2020). The sequences were deposited in GenBank (Accession Nos. OQ600619, OQ603370, OQ603373, OQ603379, OQ974177, OQ974176, OQ974178, and OQ974175). BLASTN analysis in GenBank showed that these genes exhibited 100% similarity to the sequences of Colletotrichum aenigma (MT476812, MN525817, MN525878, MN525904, MN525836, KX620296, and MN338281) and 99% similarity to the sequence of Colletotrichum sp. strain (MT071110). Concatenated sequences of these eight genes and Colletotrichum species sequences from GenBank were then used to construct a phylogenetic tree by using the maximum likelihood method in IQtree V1.5.6. Isolate JFRL 03-1005 was grouped into a clade with C. aenigma with a high bootstrap value. Thus, the isolate was identified as C. aenigma based on morphological and molecular data. To verify Koch's postulates, pathogenicity was tested on 2-year-old healthy potted plants of I. cornuta. Ten disinfected leaves were wounded with a sterile scalpel, and then inoculated with 10 μl of conidial suspension (1 × 106 conidia/ml) from isolate JFRL 03-1005. The control leaves were inoculated with 10 μl of sterile water. Then, the potted plants were incubated at 28°C with a 12 h photoperiod and 80% humidity. After 10 days, distinct spots appeared on all inoculated leaves, whereas control leaves remained asymptotic. C. aenigma was reisolated from the spots and identified by sequencing the ITS, ACT, GAPDH, TUB2, CAL, GS, APN2 and ApMat genes. Previous studies reported that C. aenigma can caused anthracnose on the leaves of various cash crops in China, such as apple, tree peonies, mulberry, and walnut (Wang et al. 2020; Zhang et al. 2021; Wang et al. 2022; Zhu et al. 2022). To the best of our knowledge, this is the first report of C. aenigma causing anthracnose on I. cornuta in China, this report further confirmed that C. aenigma has a wide range of hosts in nature. the anthracnose on I. cornuta caused by C. aenigma has seriously affected its ornamental value. Therefore, more attention should be paid to this disease and appropriate control strategies should be formulated.

Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus

ObjectivesGenus Labeo of family Cyprinidae comprising of important group of fish species are known for ornamental purpose, food, extracting oil, medicinal value and for potential viable aquaculture. The present study was conducted to assess the morphometric and molecular identification of freshwater fishes of genus Labeo including Catla catla, Labeo rohita, Labeo calbasu, Labeo gnius, Labeo bata from the three fish resources of River Indus, Punjab, Pakistan. MethodsOut of 75, thirty fish specimen were amplified and sequenced with 650 bp of mitochondrial COI gene for the evaluation of fish biodiversity, management and conservation by using different bioinformatics techniques. ResultsMaximum and minimum genetic divergence between fishes of C. catla, L. calbasu, L. boga, L. gonius and L. rohita, were 0.052 to 0.105, respectively. Highest divergence was found between Labeo bata and Labeo rohita. Interspecific mean distance was found higher than intraspecific distance. In nucleotide base composition, AT contents was higher than GC contents indicated the clear pattern of anti-G bias. Transition rate was k1 = 8.84 for purines and transversional rate was k2 = 15.47 for pyrimidines with transition/transversion bias R = 5.62. Tajima D test and nucleotide diversity was measured D = 1.382883 and π = 0.049981 respectively. Positive value of D indicated a strong selective pressure and lack of population expansion. Thirty species were identified with e-value 0.0 and similar identity 99.85 %–100 % with maximum 600 bp length. Phylogenetic tree revealed two major clades with 95 % high bootstrap values identity showed closet relationship among these species. ConclusionsCurrent study supported the efficacy of the COI gene for the species identification in River Indus and develop the concept for establishing Pakistani fish gene bank which is still needed.

Taxonomic study and diversity of Postia s.lat. in Swat, Pakistan: addition of five brown rot Polypores to the country.

Brown rot Polypores are ecologically significant as they play a crucial role in maintaining the carbon cycle and contribute to humus formation in forest ecosystems through their lignocellulose degradation ability. It is important to note that some species can significantly impact timber, potentially causing decay in economically valuable wood. Many Asian countries including Pakistan are still under the exploratory phase and have undocumented species diversity in Polypore fungi. In the current study, collections representing five different species belonging to two families, Postiaceae and Adustoporiaceae, were subjected to detailed morphoanatomical and molecular analyses. A combined matrix of two gene datasets (ITS and nrLSU) was analyzed using three different phylogenetic methods viz. Maximum Parsimony (MP), Maximum Likelihood (ML), and Bayesian inference (BI). Our study presents descriptions of five previously undocumented brown rot Polypore species from the country including Fuscopostia fragilis (Fr.) B.K. Cui, L.L. Shen & Y.C. Dai, Amaropostia stiptica (Pers.) B.K. Cui, L.L. Shen & Y.C. Dai, Cyanosporus piceicola B.K. Cui, L.L. Shen & Y.C. Dai, Spongiporus balsameus (Peck) A. David, Rhodonia placenta (Fr.) Niemelä, K.H. Larss. & Schigel. Regarding the molecular data, nodes of our subject sequences were substantially supported and fell under their respective species clades with high ML bootstrap values (≥ 95), MP bootstrap ≥ 74 and BI probabilities ≥ 0.98. Findings of the study will not only contribute to our understanding of local Polypores species diversity but also enhance knowledge of geographical distribution in global context.

Phylogenetic position of Helicotylenchus multicinctus on banana recorded in the municipality of Limoeiro do Norte, Brazil

The spiral nematode, Helicotylenchus multicinctus, is present in production areas of various agricultural crops around the world and in Brazil, standing out as the main nematode causing damage to banana cultivation. Given the importance of this pathogen, this work aimed to determine the sequence of the ITS and 28S rDNA regions of H. multicinctus and explore the phylogenetic position of H. multicinctus isolated from Brazil. After collection, nematodes were extracted from the samples and morphological and molecular identification was carried out and, through Bayesian analysis of 28S rDNA, the phylogenetic position of H. multicinctus was inferred. The morphological and molecular data of this study identified H. multicinctus associated with banana farming in Limoeiro do Norte and H. multicinctus from Brazil grouped with the other H. multicinctus isolates in the world presenting high Bootstrap values within Clade XI.

First Report of Neocosmospora mori Causing Root Rot and Stem Blight of Mulberry in Nanzhang, Hubei, China.

Mulberry (Morus alba L.) has been cultivated for thousands of years in many temperate regions in East Asia and is commonly used to feed silkworms. In May 2021, 5 to 8% incidence of stem blight on 4-year-old mulberry 'Nongsang 14' was observed in several orchards in Nanzhang County, Hubei Province, China. The roots and stems showed symptoms of vascular discoloration, and the tender new shoots, surrounded by white hyphae, were detached easily. Symptomatic stem tissues (5 mm × 5 mm) were excised from the border between diseased and healthy tissues, surface sterilized in a 75% ethanol solution for 30 s and 2.5% sodium hypochlorite for 1.5 min, washed three times in sterile distilled water, then placed on potato dextrose agar (PDA, 250 g potatoes, 2% dextrose, 1.6% agar), and incubated at 25°C in darkness. Two isolates (Bq2 and Bq3) were subcultured using the single-spore method. On PDA, colonies were cottony, with whitish aerial mycelium and the daily growth rate was 4.25 to 5.50 mm/day at 25°C in darkness. On carnation leaf agar, macroconidia were fusiform with slightly curved apical cells and foot-shaped basal cells, three to five septate, measuring 47.5 to 80.3 × 3.6 to 5.6 μm (average 68.7 × 4.7 μm, n = 30). On spezieller nährstoffarmer agar, microconidia were produced in false heads on monophialides, mostly 0-septate, oval, obovoid, or reniform in shape, measuring 5.1 to 10.7 × 2.7 to 5.3 μm (average 8.5 × 3.3 μm, n = 30). Chlamydospores were 4.9 to 11.0 μm in diameter (average 6.8 μm, n = 30), round shaped, thick-walled, and produced individually or in pairs or in chains. For molecular identification, the ribosomal internal transcribed spacers (ITS), translation elongation factor 1α (EF-1α), 28S large subunit nrDNA (LSU), and calmodulin (CAM) genes were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990), EF1H/EF2T (O'Donnell et al. 1998), LR0R/LR5 ( Vilgalys and Hester 1990; Vilgalys and Sun 1994), and CL1/CL2A (Geiser et al. 2021; Wang et al. 2011), respectively. The sequences were deposited in GenBank (OQ711943-OQ711944 for ITS, OQ722438- Q722439 for EF-1α, OQ722441-OQ722442 for CAM, and OR116152-OR116153 for LSU). A maximum-likelihood phylogenetic analysis based on multilocus sequences was conducted using MEGA7, which showed that the two isolates grouped into a clade with Neocosmospora mori (previously Fusarium solani species complex) supported by a high bootstrap value (85%), and hence, they were identified as N. mori based on morphological and molecular analyses (Brooks et al. 2022; Crous et al. 2021; Lombard et al. 2015; Zeng and Zhuang 2023). To complete Koch's postulates, three healthy 2-month-old seedlings grown in sterile peat mix were removed from pots and the roots were washed in sterile water. Each plant was inoculated by dipping wounded and unwounded roots in a spore suspension (1 × 107 conidia/ml) for 20 min, and then 10 mL of the spore suspension was poured over the roots of each seedling after transplanting. Three plants were treated with sterilized water as a control. The tested plants were then kept in a plastic box containing sterile water and incubated at 25°C in a 12 h/12 h light/dark cycle. The pathogenicity assay was repeated three times for each isolate. Root and stem blight was observed 10 days after inoculation, while the control plants were asymptomatic. Furthermore, fungi with morphological characteristics of N. mori were only reisolated from the symptomatic stems and sequences of LSU matched those of isolates Bq2 and Bq3. This pathogen has been reported previously causing stem blight on mulberry trees in Japan and South Korea (Sandoval-Denis et al. 2019), but to our knowledge, this is the first report of N. mori causing root rot and stem blight of mulberry in China. This report will facilitate the development of effective control strategies for the disease.

Hemolivia species infecting Central American wood turtles (Rhinoclemmys pulcherrima manni) and problems with differential diagnosis within the genus Hemolivia.

Blood parasites of the genus Hemolivia Petit, Landau, Baccam and Lainson, 1990 (Adeleorina: Karyolysidae) are hemogregarines of ectothermic vertebrates, such as lizards, chelonians, and toads. Only five species of Hemolivia from vertebrate hosts and one from their tick vector have been described so far. In the present study, Central American wood turtles (Rhinoclemmys pulcherrima manni) originating from Southern Nicaragua were screened for the presence of hemogregarines. Ten out of 30 specimens (33.3%) were positive for Hemolivia using both approaches - microscopy and PCR-based analyses. Phylogenetic analyses based on the 18S rRNA gene revealed the presence of two haplotypes, both placed as sister taxa in the Hemolivia clade. Their phylogenetic position was supported by high bootstrap values and high posterior probabilities, suggesting that there are at least two new distinct haplotypes corresponding to two distinct species. However, the specimens of each haplotype were microscopically indistinguishable from each other based on the gamont morphology, therefore, only a single species could be described and named, as Hemolivia pulcherrima n. sp. We consider that the uniform morphology of the most common blood stages of species of the genus Hemolivia complicates their differential diagnosis. Sequence divergence and different host spectra, therefore, remain the only differentiating tools.

Characterization of the complete chloroplast genome assembly of Amorphophallus yunnanensis Engler, Pflanzenr (Araceae) from southwestern China

Southwestern China is a biodiversity hotspot due to its diverse topography and environment. Amorphophallus yunnanensis is a species of perennial herb that is mainly distributed throughout southwestern China. The genetic diversity and divergence in this species have not been assessed largely due to a lack of genomic resources. To help with the phylogeographic study, we sequenced and assembled the first complete chloroplast genome sequence of A. yunnanensis. The length of the chloroplast genome was 164,417 bp, with an average GC content of 36% (GenBank accession no. OR400247). The genome possessed a typical quadripartite structure, and the lengths of the large single-copy (LSC), small single-copy (SSC), and two inverted repeat (IR) regions were 92,149 bp, 15,182 bp, 28,543bp, and 28,543bp, respectively. A total of 128 genes were annotated across the genome, including 82 protein-coding genes, 8 rRNAs, and 38 tRNAs. The maximum likelihood (ML) phylogeny confirmed the phylogenetic position of Amorphophallus within Araceae, with the Amorphophallus species forming a single monophyletic clade with a high bootstrap value. The ML tree also indicated that A. yunnanensis was most closely related to A. coaetaneus. This newly sequenced chloroplast genome assembly will aid in future studies of genetic diversity, historical population dynamics, and geographic differentiation patterns of A. yunnanensis.

Complete mitochondrial genome of golden variant of freshwater fish Labeo rajasthanicus (Cypriniformes: Cyprinidae): endemic to India

The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.

Empedobacter sedimenti sp. nov., isolated from sediment of East Taihu Lake.

A Gram-reaction-negative, strictly aerobic, pale yellow, non-gliding, rod-shaped bacterium, designated DT-LB-19T, was isolated from the sediment of East Taihu Lake in Jiangsu Province, PR China. Strain DT-LB-19T showed the highest 16S rRNA gene sequence similarities to members of the genera Algoriella, Chishuiella and Empedobacter (94.84-95.77 %) in the family Weeksellaceae. In phylogenetic trees based on genomes, strain DT-LB-19T clustered within the genus Empedobacter but formed a separate subclade with a high bootstrap value. The average nucleotide identity and digital DNA-DNA hybridization values between DT-LB-19T and the closely related type strains were in the range of 82.5-86.9 % and 25.8-32.3 %, respectively. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, C16 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 03-OH. The predominant menaquinone was menaquinone-6. The polar lipid profile consisted of phosphatidylethanolamine, one glycolipid, two aminophospholipids and five unidentified lipids. The DNA G+C content was 31.8 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic results, we propose that strain DT-LB-19T represents a novel species of the genus Empedobacter, for which the name Empedobacter sedimenti sp. nov. is proposed, with strain DT-LB-19T (=KCTC 82330T=CCTCC AB 2023026T= JSACC 11448T) as the type strain.