High Support Values Research Articles

Assessment of genetic diversity of Trypanosoma evansi in the domestic animal populations through ITS-1 gene sequence analysis.

Trypanosoma evansi infects domestic animals, causing a debilitating and occasionally fatal disease. The disease leads to significant economic losses to farmers and poses a substantial impediment to the growth of livestock production in developing nations, including India. Considering the challenges associated with managing this infection, there is an urgent need to enhance our understanding of the molecular and genetic diversity of T. evansi. Therefore, this study was planned to analyze the genetic diversity of T. evansi using available internal transcribed spacer-1 (ITS-1) gene sequences from India and compare them with sequences from around the globe. Blood samples used in this study were collected from naturally infected animals including dogs, cattle, and buffaloes in the Indian state of Madhya Pradesh. Using the ITS-1 gene, we amplified a 540 base pairs (bp) segment using polymerase chain reaction (PCR), sequenced it, and identified intra-specific variations. Phylogenetic analysis of 90 sequences, including 27 from India, revealed three distinct clusters with high bootstrap support values. A haplotype network analysis identified 34 haplotypes, with H7 being the most prevalent, indicating a complex evolutionary history involving multiple countries. The genetic analysis of the Indian population revealed distinct characteristics. Despite low nucleotide diversity, there was high haplotype diversity in comparison to other populations. Tajima's D, Fu and Li's D, and Fu and Li's F exhibited non-significant negative values, indicating potential stability. Additionally, the slightly positive values in Fu's Fs, Raggedness (r), and Ramos-Onsins and Rozas (R2) statistics suggested a lack of recent significant selective pressures or population expansions. Furthermore, the presence of genetic differentiation and gene flow among T. evansi populations highlighted ongoing evolutionary processes. These findings collectively depicted a complex genetic landscape, suggesting both stability and ongoing evolutionary dynamics within the Indian population of T. evansi. The findings of this study are important for understanding the evolutionary history and population dynamics of T. evansi, and they may help us develop effective control strategies.

COMPARISON OF MARKET BASKET ANALYSIS METHOD USING APRIORI ALGORITHM, FREQUENT PATTERN GROWTH (FP- GROWTH) AND EQUIVALENCE CLASS TRANSFORMATION (ECLAT) (CASE STUDY: SUPERMARKET “X” TRANSACTION DATA FOR 2021)

The retail industry continues to grow and develop in Indonesia. The retail sector as a provider of goods used in everyday life has long started digital transformation in its business. Digital technology helps the retail industry collect valuable customer data. Business analytic is the use of data, information technology and statistical analysis, which is used to obtain information about a business and make decisions based on facts. Business analytic turns data into steps or actions in the context of making business decisions. Consumer needs and purchasing behavior can be predicted with big data-based technology. Association Rule is a technique in data mining to find the relationship between items in an item set combination. One of the utilizations of the association rule method is market basket analysis. Algorithms that can be used to analyze consumer purchasing patterns include the Apriori algorithm, Frequent Pattern Growth (FP-Growth) which represents a database structure in a horizontal format, and the Equivalence Class Transformation (ECLAT) algorithm which represents a vertical data format. In addition, this research will first analyze the complexity of the algorithm based on the time complexity in running the algorithm. This analysis uses these three algorithms, which are applied to Supermarket "X" transaction data in 2021, namely 136,202 transactions. The measure of goodness that is used to find out the best algorithm uses support and confidence values. The results show that the ECLAT algorithm is the most superior algorithm compared to the others based on the execution time required by the algorithm. The support value used in forming associations in the ECLAT algorithm is 1%, resulting in 19 rules. From the results of these rules, the highest support value was generated by the purchase of Indomie goreng special and Indomie ayam bawang, where as many as 1,362 shopping transactions bought these two items together or 2.71% of the total transactions.

Comparative mitochondrial genome analysis of three leafhopper species of the genus Abrus Dai & Zhang (Hemiptera: Cicadellidae: Deltocephalinae) from China with phylogenetic implication

BackgroundThe phylogenetic position and classification of Athysanini are poorly defined, as it includes a large group of polyphyletic genera that have historically been assigned to it mainly because they still exhibit the most typical deltocephaline genitalic and external body characters but lack the distinctive characteristics that other tribes possess. The bamboo-feeding leafhopper genus Abrus belong to the tribe Athysanini of subfamily Deltocephalinae, which currently comprises 19 valid described species, and are limited to the Oriental and Palaearctic regions in China. Although the taxonomy of Abrus are well updated, the references on comparative mitogenomic analyses of Abrus species are only known for a single species. In this study, we sequenced and analyzed the complete mitochondrial genomes (mitogenomes) of Abrus daozhenensis Chen, Yang & Li, 2012 (16,391bp) and A. yunshanensis Chen, Yang & Li, 2012 (15,768bp) (Athysanini), and compared with published mitogenome sequence of A. expansivus Xing & Li, 2014 (15,904bp).ResultsThese Abrus species shared highly conserved mitogenomes with similar gene order to that of the putative ancestral insect with 37 typical genes and a non-coding A + T-rich region. The nucleotide composition of these genomes is highly biased toward A + T nucleotides (76.2%, 76.3%, and 74.7%), AT-skews (0.091 to 0.095, and 0.095), negative GC-skews (− 0.138, − 0.161, and − 0.138), and codon usage. All 22 tRNA genes had typical cloverleaf secondary structures, except for trnS1 (AGN) which lacks the dihydrouridine arm, and distinctively trnG in the mitogenome of A. expansivus lacks the TψC arm. Phylogenetic analyses based on 13 PCGs, 2 rRNA genes, and 22 tRNA genes consistently recovered the monophyletic Opsiini, Penthimiini, Selenocephalini, Scaphoideini, and Athysanini (except Watanabella graminea, previously sequenced species as Chlorotettix nigromaculatus) based on limited available mitogenome sequence data of 37 species.ConclusionAt present, Abrus belongs to the tribe Athysanini based on both morphological and molecular datasets, which is strongly supported in present phylogenetic analyses in both BI and ML methods using the six concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Phylogenetic trees reconstructed herein based on the BI and ML analyses consistently recovered monophylitic Athysanini, except Watanabella graminea (Athysanini) in Opsiini with high support values.

Optimizing Inventory with Frequent Pattern Growth Algorithm for Small and Medium Enterprises

The success of a business heavily relies on its ability to compete and adapt to the ever-changing market dynamics, especially in the fiercely competitive retail sector. Amidst intensifying competition, retail business owners must strategically manage product placement and inventory to enhance customer service and meet consumer demand, considering the challenges of finding items. Poor inventory management often results in stock shortages or excess. To address this, adopting suitable inventory management techniques is crucial, including techniques from data mining, such as association rule mining. This research employed the FP-Growth algorithm to identify patterns in product placement and purchases, utilizing a dataset from clothing store sales. Analyzing 140 transactions revealed 24 association rules, comprising rules with 2-itemsets and frequently appearing 3-itemset rules. The highest support value in the final association rules with 2-itemsets was 10% with a confidence level of 56%, and the highest support value in the 3-itemsets was 67% with the same confidence level. Additionally, three rules had a confidence level of 100%. Thus, the association rules generated by the FP-Growth frequent itemset algorithm can serve as valuable decision support for sales of goods in small and medium-sized retail businesses.

Diaporthe melongenae sp. nov, a new fungal species causing leaf blight in eggplant

AbstractEggplant is a vegetable crop of the Solanaceae family. In November 2021, leaf blights of eggplant were observed from an eggplant field with an approximate disease incidence of 10%–30% in Cavite, Philippines. The infected leaves had typical symptoms of Phomopsis blight disease. Two fungal isolates were obtained, and morphological characteristics resemble those of a Diaporthe species. Based on the combined multi‐gene phylogenetic analysis, Diaporthe melongenae sp. nov. formed a separate clade from closely related species: D. guangdongensis, D. melonis and D. moriniae with high bootstrap support values of 99/1.0 ML/PP. Moreover, the morphological characteristics of D. melongenae have differences from the closely related species. D. melongenae differs by having a slightly smaller average alpha conidial size than D. guangdongensis and absence of beta conidia. Diaporthe melonis is distinct from D. melongenae by having slightly constricted middle alpha conidia. Together, based on morphology, multi‐locus phylogeny, GCPSRA and ecology (lifestyle, host and pathogenicity) herein we introduce D. melongenae as a novel species. Furthermore, this study presented the current phylogenetic tree of D. sojae species complex based on accepted Diaporthe species.

In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data

BackgroundMacrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination “M. amazonicum complex” is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará.ResultsSequences were obtained from the prawn’s transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91–100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial).ConclusionsIt was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.

Systematic studies on some West African species of the Tribe Bauhinieae (Cercidioideae)

The tribe Bauhinieae is the largest and most taxonomically complex group within the subfamily Cercidoideae. They possess the most distinguishable morphological features but are the most variable group. Here, we explore the phylogenetic relationship of the tribe Bauhinieae using morphological, anatomical and molecular data (ITS, rbcL, trnL-F, ITS+rbcL+trnL-F). Relationships inferred from morphological, anatomical and molecular data revealed congruent result, a non-monophyletic Bauhinia and Piliostigma group. The leaf epidermal shape in all Bauhinia species examined are polygonal with straight cell walls except B. tomentosa, which has an undulating cell wall. Stomatal types observed vary between the two genera studied. Bauhinia species has paracytic stomata while Piliostigma species exhibited hemiparacytic stomata. Dendrogram generated revealed the interrelationship between the species at a distance value of 80. Bayesian analysis revealed a high resolution of species and posterior probability. The strict consensus tree for all the tested gene regions revealed a polyphyletic Bauhina divided into three major clades. The Piliostigma group exhibited a paraphyletic and polyphyletic relationship within the Bauhinia group at high support values. B tomentosa exhibited a closer relationship with Piliostigma species. These results support the proposition to divide members of the large Bauhinia s.s group into subclades. This study has attempted to elucidate the unresolved species and genus level taxonomy of the tribe Bauhinieae. However, more variable gene regions in addition to broader species sampling should be considered for further phylogenetic patterns of this taxon.

A new freshwater amphipod (Amphipoda, Gammaridae) from the Fakıllı Cave, Düzce Türkiye: Gammarus kunti sp. nov.

Aquatic species (such as fish, amphipods, isopods, hirudineans etc.) adapted to environmental conditions can live in caves connected to groundwater. The species of Niphargus and Gammarus are the most commonly encountered amphipods in caves. Türkiye is very rich in terms of karst areas and is home to more than 2000 known caves. Fakıllı Cave, located in Düzce Province in the Western Anatolian Region, has a length of 1071 m. A new amphipod species belonging to the Gammarus genus has been identified from the cave and named as Gammarus kuntisp. nov. Some of the characteristic features of the newly-identified species can be listed as “Medium-large size; smooth body, well-developed and reniform eyes; non-prolonged extremities; antennal gland cone is straight and long; second antenna with setose peduncular and flagellar segments; medial palmar spine present; posterior margin of pereopod 3 densely setose; anterior margins of pereopods 6 and 7 armed with spines only; epimeral plates not pointed”. Although the mentioned features are generally seen in epigean species, the members of this species were sampled from the dark zone of the Fakıllı Cave. The partial sequences of the COI (573 bp) and 28S (914 bp) genes of the newly-described species, Gammarus kuntisp. nov., were generated. The pairwise genetic distances between the new species, Gammarus kunti sp. nov. and other species ranged from a minimum of 16.23% (G. tumaf) to a maximum of 28.27% (G. roeselii) for the COI gene and a minimum of 0.88% (G. tumaf) to a maximum of 6.81% (G. balcanicus) for the 28S gene. Phylogenies generated by the NJ and ML methods, based on the combined data, assigned the new species as an independent lineage with high support values. In addition, the ASAP method identified the new species as a single MOTU independent of other species. G. tumaf and G. baysali are the sister taxa of G. kuntisp. nov. Detailed descriptions and drawings of the extremities of the male holotype and the female allotype are given and the morphology of the newly-identified species is compared with its relatives.

Analysis of the Application of Transaction Data with Association Techniques using the Apriori Algorithm in Pharmacy

The development of information technology influences the rapid growth in the amount of data collected and stored in large t. Dimas Pharmacy, located at Jl. Segara Kec. Nipah Panjang is one of the public health services that sells various medicines, medical devices, and so on. This study is expected to provide positive benefits for owners of Dimas Nipah Panjang Pharmacy in Providing information about the pattern of medicine purchases made by consumers and Facilitating pharmacy owners to know the available medicine supplies in the warehouse so as not to experience emptiness when needed. Problem Formulation, Literature Study, Data Collection, Calculation and Analysis of Associations with Priori Algorithms, Results Evaluation and Analysis and Report Making. Based on the results of interviews and observations that have been made, the authors obtain data from the Dimas Pharmacy sales transaction. Data held ± 1000 sales transaction data for the period of May and June. But the author only entered 216 sales transactions in May and 141 sales transactions in June. After knowing the method of data selection, the authors conducted data selection by taking 6 items of significant data specifications in certain contexts, namely Anti Serotonin / Allergy, Antacid / Ulcer, Antibiotics, Antipyretics, Inflammation, Hypertension Each of these items had different brands. From these results it can be explained that the sales transaction of the Dimas Pharmacy in May and June generates or generates relationships between shopping product items. With the calculation of the Apriori Association Algorithm, a Market Basket Analysis relationship was found between Medicinal Pronicy and Dexa items. With the Rule "IF Buy Pronicy, THEN Buy Dexa". The rule is generated from the highest support and confident values of the overall support and confident items. The highest support value is 0.15 and the highest confident value is 0.5 ".

Phylogenetic analysis of rabies surveillance samples from north and northeast Brazil.

Viruses of the Lyssavirus genus are classified into several genotypes (GT1 to GT7), of which only GT1 (classic rabies virus-RABV) has a cosmopolitan distribution and circulates in Brazil. GT1 is subdivided into several antigenic variants (AgV) maintained in independent cycles with a narrow host range and distinct geographic distributions, namely, AgV1 and AgV2 found in dogs, AgV3 in the vampire bats Desmodus rotundus, and AgV4 and AgV6 in bats non-hematophagous Tadarida brasiliensis and Lasiurus cinereus, a common variant of marmoset (Callithrix jacchus), and crab-eating fox (Cerdocyon thous). In this study, we performed phylogenetic analysis to identify at the antigenic variant level; six RABV genomes derived from the Rabies Surveillance in the north and northeast regions of Brazil. The analysis resulted in the formation of 11 monophyletic clusters, each corresponding to a particular variant, with high bootstrap support values. The samples were positioned inside the AgV3, AgV6, and Callithrix variant clades. This is the first report of the AgV6 variant found in northern Brazil, which provides valuable information for rabies surveillance in the country. The possibility of viral spillover has been much debated, as it deals with the risk of shifting transmission from a primary to a secondary host. However, more genomic surveillance studies should be performed, with a greater number and diversity of samples to better understand the transmission dynamics of each variant to detect changes in its geographic distribution and spillover events.

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae).

Japanagallia is a genus of Cicadomorpha in the family of leafhoppers that are plant piercing-sucking insects, and it is difficult to distinguish by morphological characteristics. So far, only one complete mitochondrial genome data has been reported for the genus Japanagallia. Therefore, in order to better understand this group, we assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. Nucleotide composition analysis showed that AT content was higher than GC content, and the protein-coding sequences preferred to end with A/T at the third codon position. Relative synonymous codon usage analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed the codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure. In the neutrality plot, the slopes of regression lines were < 0.5, suggesting that natural selection was playing a major role while mutation pressure was of minor importance. The effective number of codons showed that the codon usage bias between genes and genomes was low. Correspondence analysis revealed that the codon usage pattern differed among 13 protein-coding genes. Phylogenetic analyses based on three datasets using two methods (maximum likelihood and Bayesian inference), restored the Megophthalminae monophyly with high support values (bootstrap support values (BS) = 100, Bayesian posterior probability (PP) = 1). In the obtained topology, the seven Japanagallia species were clustered into a monophyletic group and formed a sister group with Durgade. In conclusion, our study can provide a reference for the future research on organism evolution, identification and phylogeny relationships of Japanagallia species.

First Report of Cobweb Disease in Auricularia cornea var. Li. Caused by Hypomyces mycophilus in China.

Auricularia cornea var. Li. is a natural mutation strain of A. cornea which has been preferred by consumers for its white colour, good taste and pharmacological properties (Rebecca et al. 2020). In October 2021, a disease with symptoms similar to that of cobweb disease (Carrasco et al. 2017) was observed in A. cornea var. Li. in four mushroom farms in Fangshan District (115.83°E, 39.55°N), Beijing, China, infecting 20% of the fruiting bodies (Fig. 1A-D). White cottony mycelia formed typically on the casing soil and they gradually spread to the stipes and pileus, covering the whole fruiting body, which eventually died and lost commodity value. Cultures were obtained by aseptically transferring the diseased fruiting bodies onto potato dextrose agar (PDA); they were deposited in the culture collection (ID: JZBQA3) of the Beijing Academy of Agriculture and Forestry Sciences, China. The colonies were floccose with aerial mycelium white. Purplish grey diffusing pigments occasionally formed on the reverse side of the plate at 25 °C (Fig. 2A-B). Conidiophores arising in aerial mycelium, indefinite in length, branches septate, each cell producing denticulate conidiogenous loci, each denticle bearing a single conidium. Conidia mostly oblong to ellipsoidal, smooth, (9.0-)9.9-17.0(-18.0)×(6.0-)6.9-10.2 μm (n = 60), 0~1 septate (Fig. 2C-E). Chlamydospores forming as lateral branches of hyphae were commonly observed, globose, ellipsoid or oblong, 14.8-22×14.7-19.6 μm, l/w = 1.0-1.3 (Fig. 2F-G). The morphological characteristics were consistent with that of Hypomyces mycophilus, whose anamorph was Cladobotryum polypori (Rogerson et al. 1993, Zeng et al. 2017). For further species identification, genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen, USA). The internal transcribed spacer (ITS) regions and large subunit ribosomal RNA (LSU) genes were amplified using the primer pairs ITS1/ITS4 (White et al. 1990) and LROR/LR5 (Bhattacharya et al. 2000), respectively. The sequences were deposited in GenBank with accession numbers OP430530 and OP430531. BLAST nucleotide searches showed more than 99% homology with corresponding sequences of Hypomyces mycophilus HMAS 275554 and CBS 175.56. Phylogenetic trees based on ITS and LSU revealed that the strain JZBQA3 was grouped with H. mycophilus with high support value (Fig. 3). A in vivo pathogenicity test was performed using eight mushroom sticks with healthy fruiting bodies in triplicate. Each four sticks were sprayed with conidial suspension (108 spores/mL) of strain JZBQA3 or sterile distilled water, respectively, and maintained in an artificial climate chamber at 25-26°C. Cobweb-like characteristics were observed on the fruiting bodies treated with the JZBQA3 conidial suspension 2-3 days after inoculation, while those treated with sterile distilled water remained symptomless (Fig. 4 A-B). The same pathogen was re-isolated and confirmed from the infected fruiting bodies by integrated analysis of morphological characteristics and gene sequencing data, fulfilling Koch's postulates. Hypomyces mycophilus was first reported on Trametes versicolor in North Carolina (Rogerson et al. 1993), and is the causal agent of cobweb diseases on Auricularia heimuer (Zhang et al. 2023). To our knowledge, this is the first report of cobweb disease caused by H. mycophilus in A. cornea var. Li. This finding is a valuable contribution to the knowledge of cobweb disease development in edible fungi.

The larval, pupal and mitogenomic characteristics of Agrilusadelphinus Kerremans, 1895 (Coleoptera, Buprestidae) from China.

In this study, the larva and pupa of Agrilusadelphinus are described and illustrated. DNA barcoding (COI gene) was used to associate the larval and pupal stages with adults based on the maximum-likelihood method. In the resulting phylogenetic tree, species from the same species-group were found to be clustered on a branch with high support value. To better understand A.adelphinus, the complete mitochondrial genome of this species was also sequenced and annotated. Comparing this genome to the known mitogenomes of Agrilus species, the newly sequenced genome is shorter, with 15,732 bp. However, its whole mitogenome composition and gene orientation were consistent with that of most species of Buprestidae. In the mitogenome of A.adelphinus, the ATGATAG sequence was observed between ATP8 and ATP6, which is ATGATAA in other insect mitogenomes. Leu2, Phe, Ile, Gly, and Ser2 were the five most frequently encoded amino acids. The results further prove that DNA barcoding can remove the limitation of traditional taxonomy which cannot identify to species all developmental stages. This study also provides valuable molecular and morphological data for species identification and phylogenetic analyses of the genus Agrilus.

Complete mitochondrial genome and phylogenetic analysis of Sineleotris saccharae (Perciformes, Odontobutiae)

The freshwater sleeper, Sineleotris saccharae Herre, 1940 is a member of the Odontobutiae family, widely distributed in southern China. In the present study, we determined the complete mitochondrial genome of S. saccharae for the first time and analyzed its evolutionary relationship. The complete mitochondrial genome of S. saccharae was 16,487 bp long, and had 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNA (rRNAs) and a control region (CR). The mitogenome of S. saccharae shared the same gene organization and orientation as other teleosts. According to phylogenetic research, S. saccharae was sister to S. chalmersi with high support value, providing the monophyly of the genus Sineleotris. These results will be helpful for understanding the systematics of the odontobutids.

Mitogenomic phylogeny of nymphalid subfamilies confirms the basal clade position of Danainae (Insecta: Lepidoptera: Nymphalidae).

The phylogenetic relationships among the nymphalid subfamilies have largely been resolved using both morphological and molecular datasets, with the exception of a conflicting basal clade position for Libytheinae or Danainae that remains contentious between morphological and molecular studies. Several phylogenomic analyses have found that the danaine clade is sister to other nymphalid subfamilies; however, it largely depends on utilizing different molecular datasets, analysis methods, and taxon sampling. This study aimed to resolve the basal clade position and relationships among subfamilies and tribes of Nymphalinae by combining the most comprehensive available mitogenomic datasets with various analyses methods by incorporating a new Symbrenthia lilaea Hewitson sequence data. Phylogenetic relationships among 11 nymphalid subfamilies and the tribes of Nymphalinae were inferred by combining new and available mitogenomic sequence data from 80 ingroup and six outgroup species. The phylogenetic trees were reconstructed using maximum-likelihood (ML) and Bayesian inference (BI) methods based on five concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Danainae is well-supported as the basal clade and sister to the remaining nymphalid subfamilies, except for the paraphyletic Libytheinae. Libytheinae was either recovered as a sister to the danaine clade followed by the satyrine clade or sister to the nymphaline + heliconiine clades, and is consistent with recent phylogenetic studies on Nymphalidae. The monophyletic Nymphalinae has been recovered in all analyses and resolves tribal-level relationships with high support values in both BI and ML analyses. We supported the monophyletic Nymphalini as a sister clade to Victorini, Melitaeini, and Kallimini + Junoniini with high supporting values in BI and ML analyses, which is consistent with previously published morphological and molecular studies.

Varicosporellopsis shangrilaensis sp. nov. (Nectriaceae, Hypocreales), a new terricolous species isolated from the rhizosphere soil of Astragalus polycladus in northwestern Yunnan, China

Two fungal strains were isolated from the rhizosphere soil of a Chinese medicinal herb plant, Astragalus polycladus, in northwestern Yunnan, China. Both of them were identified as a new fungal species of Varicosporellopsis based on the evidence of morphology and phylogenetic analysis of ITS, LSU, TUB and ACT sequences data. Phylogenetic analysis of combined ITS and LSU sequence data revealed that strains MTF 7 and KLF 01 belong to the genus Varicosporellopsis with the highest sequence similarity (95.51%) to the type strain V. americana CBS 148257 and formed a sister lineage to V. americana CPC 40768 with high support values (100% ML, 1.00 BI). Morphologically, V. shangrilaensis is characterized by macronematous, branched conidiophores, phialidic conidiogenous cells, reniform macroconidia and spherical microconidia. This new species is the first reported of Varicosporellopsis in China. The morphological description, illustrations and phylogenetic analysis of V. shangrilaensis are provided in this study.

Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae)

Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the “Chinese” clade and the “Himalayan” clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the “Chinese” clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the “Chinese” clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.

A new species of Sedum (Crassulaceae) from Mount Danxia in Guangdong, China.

Sedumjinglanii, a new species of Crassulaceae from Mount Danxia in Guangdong, China, is described and illustrated. Phylogenetic analysis based on the internal transcribed spacer (ITS) region of nrDNA suggests that the new species belongs to S.sect.Sedum sensu Fu and Ohba (2001) in the "Flora of China", and is sister to a clade comprising S.alfredi and S.emarginatum with high support values (SH-aLRT = 84, UFBS = 95) but is distantly related to S.baileyi. The new species is morphologically similar to S.alfredi but it can be distinguished from the latter in its opposite leaves (vs. alternate leaves), its usually wider leaves (0.4-1.2 cm vs. 0.2-0.6 cm), its usually shorter petals (3.4-4.5 mm vs. 4-6 mm), its shorter nectar scales (0.4-0.5 mm vs. 0.5-1 mm), its shorter carpels (1.5-2.6 mm vs. 4-5 mm), and its shorter styles (0.6-0.9 mm vs. 1-2 mm). The new species can be easily distinguished from S.emarginatum which both have opposite leaves by its short, erect or ascending rhizome (vs. long and prostrate rhizome in the latter), shorter petals (3.4-4.5 mm vs. 6-8 mm) and shorter carpels (1.5-2.6 mm vs. 4-5 mm). It can also be easily distinguished from S.baileyi by its short, erect or ascending rhizome (vs. long and prostrate rhizome) and its shorter style (0.6-0.9 mm vs. 1-1.5 mm).

Comparative analysis of the complete plastomes of nine Pimpinella species (Apiaceae) from China.

Pimpinella L. is one of the large genera in the Apiaceae family. In a previous study, the molecular phylogenies of Pimpinella were explored using nuclear ribosomal DNA internal transcribed spacers (ITS) and several chloroplast DNA segments. There have been few studies conducted on chloroplast genomes in Pimpinella, which has limited systematic understanding of this genus. We assembled the complete chloroplast genomes of nine Pimpinella species from China using data generated from next generation sequencing (NGS). The chloroplast (cp) DNA used were standard double-stranded molecules, ranging from 146,432 base pairs (bp) (P. valleculosa) to 165,666 bp (P. purpurea) in length. The circular DNA contained a large single-copy (LSC) region, small single-copy (SSC) region, and pair of inverted repeats (IRs). The cp DNA of the nine species contained 82-93 protein-coding genes, 36-37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes, respectively. Four species (P. smithii, P. valleculosa, P. rhomboidea, and P. purpurea) exhibited striking distinctions in genome size, gene number, IR boundary, and sequence identity. We confirmed the non-monophyly of the Pimpinella species on the basis of the nine newly identified plastomes. The distant relationship between the above-mentioned four Pimpinella species and Pimpinelleae was indicated with high support values. Our study provides a foundation for future in-depth phylogenetic and taxonomic studies of genus Pimpinella.

Phylogenomics and phylogeography of Menispermum (Menispermaceae).

Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. Menispermum L. (Menispermaceae) consists of three species, M. dauricum DC., M. canadense L., and M. mexicanum Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether M. mexicanum is a distinct species, a variety of M. dauricum, or simply a synonym of M. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses. In this study, we examined phylogenomics and phylogeography of Menispermum across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of Menispermum and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family. Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that Menispermum clusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense + M. mexicanum). However, M. mexicanum is nested within M. canadense and, as a result, we support that M. mexicanum is a synonym of M. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK, ycf1), four introns (trnK intron, rpl16 intron, rps16 intron, ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA, ndhF-rpl32, trnK-rps16, and trnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.