Search Results (410)

Members of the genus Nemipterus are economically important fish species distributed in the tropical and subtropical Indo-West Pacific region. The majority of species in this genus inhabit waters with sandy–muddy substrates on the continental shelf, although different species are found at slightly varying water depths. In this study, we sequenced seven species within the genus Nemipterus after identifying the specimens using complementary morphological analysis and DNA barcoding. Each species yielded over 40,000,000 clean reads, totaling over 300,000,000 clean reads across the seven species. A total of 276,389 unigenes were obtained after de novo assembly and a total of 168,010 (60.79%) unigenes were annotated in the protein database. The comprehensive functional annotation based on the KOG, GO, and KEGG databases revealed that these unigenes are mainly associated with numerous physiological, metabolic, and molecular processes, and that the seven species exhibit similarity in these aspects. By constructing a phylogenetic tree and conducting divergence time analysis, we found that N. bathybius and N. virgatus diverged most recently, approximately during the Neogene Period (14.9 Mya). Compared with other species, N. bathybius and N. virgatus are distributed in deeper water layers. Therefore, we conducted selection pressure analysis using these two species as the foreground branches and identified several environmental-responsive genes. The results indicate that genes such as aqp1, arrdc3, ISP2, Hip, ndufa1, ndufa3, pcyt1a, ctsk, col6a2, casp2 exhibit faster evolutionary rates during long-term adaptation to deep-water environments. Specifically, these genes are considered to be associated with adaptation to aquatic osmoregulation, temperature fluctuations, and skeletal development. This comprehensive analysis provides valuable insights into the evolutionary biology and environmental adaptability of threadfin breams, contributing to the conservation and sustainable management of these species. Full article

Due to the potential role of Auchenorrhyncha in the transmission of the bacterium Xylella fastidiosa in a wide variety of cultivations, during recent years in Europe, many studies have focused on species composition, abundance and seasonal appearance of Auchenorrhyncha. However, females and nymphs are difficult to identify, as species-level identification relies primarily on male genitalia morphology. Sampling was conducted over four years in olive fields in Lesvos Island, in the Northeast Aegean, Greece, using sweep nets and Malaise traps. Both adults and nymphs were collected, with males identified to species level, while females and nymphs were separated on different morphotypes. Representatives from each morphotype and identified adults were sequenced using the mitochondrial cytochrome oxidase subunit I (COI) gene. Using a classical morphological approach, 58 species were identified to species level, and using DNA barcoding, nymph morphotypes and females were successfully identified within the families Cicadellidae, Aphrophoridae, Delphacidae and Issidae. A phylogenetic tree was generated, clustering nymphs together with the corresponding adults. Our results demonstrate the utility of combining morphological and molecular methods for accurate species identification and highlight the importance of enriching online databases with additional species records. Full article

Madagascar harbors a rich marine biodiversity, yet detailed knowledge of its fish species remains limited. Of the 1689 species listed in 2018, only 22% had accessible cytochrome oxidase I (COI) sequences in public databases. In response to growing pressure on fishery resources, this study aims to strengthen biodiversity monitoring tools. Its objectives were to enrich the COI database for Malagasy marine fishes, create the first 12S reference library, and evaluate the taxonomic resolution of different 12S metabarcodes for eDNA analysis, namely MiFish, Teleo1, AcMDB, Ac12S, and 12SF1/R1. An integrated approach combining morphological, molecular, and phylogenetic analyses was applied for specimen identification of fish captured using various types of fishing gear in Toliara and Ranobe Bays from 2018 to 2023. The Malagasy COI database now includes 2146 sequences grouped into 502 Barcode Index Numbers (BINs) from 82 families, with 14 BINs newly added to BOLD (The Barcode of Life Data Systems), and 133 cryptic species. The 12S library comprises 524 sequences representing 446 species from 78 families. Together, the genetic datasets cover 514 species from 84 families, with the most diverse being Labridae, Apogonidae, Gobiidae, Pomacentridae, and Carangidae. However, the two markers show variable taxonomic resolution: 67 species belonging to 35 families were represented solely in the COI dataset, while 10 species from nine families were identified exclusively in the 12S dataset. For 319 species with complete 12S gene sequences associated with COI BINs (Barcode Index Numbers), 12S primer sets were used to evaluate the taxonomic resolution of five 12S metabarcodes. The MiFish marker proved to be the most effective, with an optimal similarity threshold of 98.5%. This study represents a major step forward in documenting and monitoring Madagascar’s marine biodiversity and provides a valuable genetic reference for future environmental DNA (eDNA) applications. Full article

The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical crops (actinidia, feijoa, citrus, and tea). A total of 47 accessions (elite cultivars, forms, and breeding lines) of these four genera were included in the study. The efficiency of the following universal primers was assessed using Sanger sequencing: ITS-p5/ITS-u4, ITS-p5/ITS-u2, ITS-p3/ITS-u4, 23S,4.5S&5S, 16S, petB/petD, rpl23/rpl2.l, rpl2 intron, rpoC1 intron, trnK intron, and trnE-UUC/trnT-GUU. Among these primers, trnE-UUC/trnT-GUU showed greater intraspecific polymorphisms, while rpl2 intron and 16S displayed the lowest polymorphism levels in all crops. In addition, the 23S,4.5S & 5S, and rpoC1 intron were efficient for intraspecific analysis of tea and actinidia species. Using five efficient chloroplast primers, a total of 22/6 SNPs/InDels were observed in tea accessions, 45/17 SNPs/InDels in actinidia, 23/3 SNPs/InDels in mandarins, and 5/4 SNPs/InDels in feijoa. These results will be useful for the further development of DNA barcodes of related accessions. Full article

Diaeretiella rapae (McIntosh, 1855) is a cosmopolitan koinobiont endoparasitoid of aphids, occurring mainly on crucifers and cereals. From description, it has changed several genera and has about 20 synonyms. The specimens for this study were collected between 1989 and 2023 from sites across Europe and the Middle East. For molecular analysis, the barcode mitochondrial gene COI was used, and morphological analysis was conducted with other Aphidius species. Morphologically, D. rapae falls within the determined variability of the same characters of the genus Aphidius. Dieretiella rapae comprised 23 haplotypes with a mean genetic distance between haplotypes of 0.8%. Phylogenetically, D. rapae is nested within Aphidius species with a genetic distance of 2.1% to 11.3%, which is within the range of other Aphidius species. Our results on morphological and molecular level confirm that D. rapae belongs to the genus Aphidius. Full article

This study reports the first record of Lyconus brachycolus in Spanish waters. A single specimen measuring 216 mm in total length was captured on 13 October 2024 in the Cantabrian Sea (north of Spain, 43.8467 N, −6.2109 W) by bottom trawl at a depth of 412 m. A detailed morphological description, updated characteristics, and illustrations are provided. For comparative purposes, an update of the species’ morphological characteristics was carried out. In an integrative taxonomic approach, the DNA barcode was obtained, which confirmed the morphological identification of the specimen as Lyconus brachycolus. A molecular taxonomic analysis using this marker showed the existence of two clades separated by 5.1%, corresponding to Lyconus brachycolus and Lyconus pinnatus, the two currently valid species of the genus. Full article

Fusarium spp. represent a critical threat to maize production and food safety due to their mycotoxin production. This study introduces a refined molecular identification protocol integrating four genomic regions—ITS1, IGS, TEF-1α, and β-TUB—for robust species differentiation of Fusarium spp. isolates from post-harvest maize in Bulgaria. The protocol enhances species resolution, especially for closely related taxa within the Fusarium fujikuroi species complex (FFSC). A newly optimized multiplex PCR strategy was developed using three primer sets, each designed to co-amplify a specific pair of toxigenic genes: fum6/fum8, tri5/tri6, and tri5/zea2. Although all five genes were analyzed, they were detected through separate two-target reactions, not in a single multiplex tube. Among 17 identified isolates, F. proliferatum (52.9%) dominated, followed by F. verticillioides, F. oxysporum, F. fujikuroi, and F. subglutinans. All isolates harbored at least one toxin biosynthesis gene, with 18% co-harboring genes for both fumonisins and zearalenone. This dual-protocol approach enhances diagnostic precision and supports targeted mycotoxin risk management strategies. Full article

Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed Brillia (Diptera: Chironomidae). We analyzed cytochrome c oxidase subunit I (COI) sequences of 241 specimens belonging to 13 Brillia species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes. Our integrated approach included genetic distance analysis, haplotype network construction, and ecological niche modeling. The results revealed remarkable cryptic diversity, with sequences clustering into 30 Barcode Index Numbers and 158 unique haplotypes, most being region-specific. Notably, East Asian and North American populations showed complete genetic distinctness, suggesting long-term isolation. Environmental factors, particularly temperature and precipitation gradients, were identified as key drivers of this diversification. The study also corrected several misidentifications in existing databases. These findings significantly advance our understanding of Brillia diversity and provide a reliable molecular tool for freshwater ecosystem monitoring, with important implications for biodiversity conservation and environmental assessment. Full article

Dioryctria Zeller, 1846 (Lepidoptera: Pyralidae) is a significant genus whose species primarily infest coniferous trees and are predominantly distributed across the Northern Hemisphere. To date, 17 species within this genus have been recorded in China. This study reports the discovery of Dioryctria simplicella (Heinemann, 1863) in China. During field surveys in forests of Heilongjiang Province, D. simplicella was observed infesting the cones and trunks of Pinus sylvestris var. mongolica Litv. as larvae. Comprehensive morphological descriptions and diagnostic characteristics of the adult, larva, pupa, and egg stages of D. simplicella are provided herein to facilitate accurate species identification within the genus. Molecular phylogenetic analysis based on mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding sequences was conducted to assess the phylogenetic position of D. simplicella within Dioryctria. These results strongly support its species identity and clarify its phylogenetic relationships with congeners. This discovery not only expands the known diversity of Lepidoptera in China but also provides new data supporting taxonomic and phylogenetic studies of the genus Dioryctria. Full article

Complete chloroplast genome sequences are widely used in the analyses of phylogenetic relationships among angiosperms. As a species-rich genus, species diversity centers of Saxifraga L. include mountainous regions of Eurasia, such as the Alps and the Qinghai–Tibetan Plateau (QTP) sensu lato. However, to date, datasets of chloroplast genomes of Saxifraga have been concentrated on the QTP species; those from European Alps are largely unavailable, which hinders comprehensively comparative and evolutionary analyses of chloroplast genomes in this genus. Here, complete chloroplast genomes of 19 Saxifraga species were de novo sequenced, assembled and annotated, and of these 15 species from Alps were reported for the first time. Subsequent comparative analysis and phylogenetic reconstruction were also conducted. Chloroplast genome length of the 19 Saxifraga species range from 149,217 bp to 152,282 bp with a typical quadripartite structure. All individual chloroplast genome included in this study contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs. The IR boundaries keep relatively conserved with minor expansion in S. consanguinea. mVISTA analysis and identification of polymorphic loci for molecular markers shows that six intergenic regions (ndhC-trnV, psbE-petL, rpl32-trnL, rps16-trnQ, trnF-ndhJ, trnS-trnG) can be selected as the potential DNA barcodes. A total of 1204 SSRs, 433 tandem repeats and 534 Large sequence repeats were identified in the 19 Saxifraga chloroplast genomes. The codon usage analysis revealed that Saxifraga chloroplast genome codon prefers to end in A/T. Phylogenetic reconstruction of 33 species (31 Saxifraga species included) based on 75 common protein coding genes received high bootstrap support values for nearly all identified nodes, and revealed a tree topology similar to previous studies. Full article

Dictyocaulosis is a parasitic disease that affects ungulate species, including red deer (Cervus elaphus). The genus Dictyocaulus comprises eighteen species, but only four have been reported to infect red deer. The disease is characterized by respiratory tract infection, particularly in the lungs, bronchi, and bronchioles, leading to inflammatory and hemorrhagic microscopic lesions, as well as emphysema and edema. The biological cycle involves a female ovipositing larvated eggs in the bronchi and trachea, which are expelled to the exterior through coughing or feces, releasing L1 into the environment. In this study, 106 adult red deer were collected from seven locations in Extremadura (Spain). Eight positive lungs were initially assessed by morphological identification, revealing a mean intensity of 13.3 adult worms per infected lung, with a global decrease to an average of 1.8 adult worms per sampled lung. The presence of adult worms in the upper and middle respiratory tract was confirmed through anatomopathological analysis. Molecular identification was performed by sequencing the COI gene. The results indicated the presence of three genetic groups, supported by significant subdivision using the ɸ_ST measure. D. cervi and D. viviparus exhibited their respective matrilineal ancestry, while D. eckerti and D. cervi demonstrated matrilineal sharing. Consequently, the possibility of introgression between these two species was suggested. Although D. viviparus had previously been identified in the same Spanish region based on morphological characteristics, D. cervi and D. eckerti were reported for the first time in the explored geographic area. Full article

Mangrove-associated fungi represent a diverse but understudied group of eukaryotic organisms, especially in the Neotropics. The Colombian Pacific region, with approximately 1300 km of coastline covered with 194,880 ha of mangrove forests that remain largely unexplored for macrofungal diversity, is recognized as a global biodiversity hotspot. This study aimed to catalog the macrofungi associated with mangrove ecosystems in Colombia, integrating morphological characterization and molecular phylogenetics, focusing on three Valle del Cauca Pacific coast localities. A total of 81 specimens were collected from both living trees and decaying wood. Detailed macroscopic and microscopic analyses were conducted, and DNA sequences from two ribosomal DNA barcode regions (ITS and LSU) were generated for 43 specimens. Three new species—Neohypochnicium manglarense, Phlebiopsis colombiana, and Porogramme bononiae—were documented. In addition, eight species were reported as new records for both Colombia and mangrove ecosystems, including Microporus affinis, Paramarasmius palmivorus, Phlebiopsis flavidoalba, Porogramme brasiliensis, Resinicium grandisporum, Trametes ellipsospora, T. menziesii, and T. polyzona. Although previously recorded in Colombian terrestrial ecosystems, Lentinus scleropus and Oudemansiella platensis are globally reported here for the first time from mangrove habitats. Furthermore, Fomitopsis nivosella and Punctularia strigosozonata were documented for the first time in Colombia. This study addresses the first exploration of mangrove-associated macrofungi in the country and provides new insights into the hidden fungal diversity and potential of mangrove ecosystems as a latent niche for basidiomycete dispersal along Colombia’s Pacific coast. Full article

Insect mitochondrial genomes are vital to understanding evolutionary relationships and identifying species. This study focused on Microtendipes (Chironomidae), a genus with unresolved phylogenetic positioning and cryptic species challenges. We sequenced and analyzed eight mitogenomes from five Microtendipes species, integrating 23 published Chironominae mitogenomes to reconstruct phylogenies using Maximum Likelihood and Bayesian Inference. The mitogenomes exhibited conserved gene arrangements but variable control region lengths (338–1266 bp) and high AT content (94.14–96.42% in control regions). Our results show that Microtendipes species may be a separate group within the subfamily, while also supporting the monophyly of the Harnischia, Polypedilum, and Chironomus complexes. The monophyly of Microtendipes bimaculus was weakly supported, which may demonstrate the presence of two potential cryptic species. Notably, larval morphology-based species groupings conflicted with the molecular data, suggesting that classifications derived from larval morphological traits may be unreliable. This study advances the evolutionary understanding of Chironomidae and underscores the limitations of single-gene barcodes in species-rich genera. Full article

Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) is the only genus within its family endemic to Brazil, being present in the Atlantic Forest and sections of the Cerrado. Taxonomic knowledge of the genus is incomplete, especially for nymphs. An integrative approach to the description of species and semaphoronts is essential for further studies. We describe a new species of Kempnyia based on morphological and molecular data, associate and describe the nymphs of both the new species and Kempnyia umbrina Froehlich, 1988, as well as expand its distribution and correct past mistakes in identification of K. umbrina. Specimens were identified morphologically and sequenced for the barcode region of the cytochrome oxidase subunit I (COI) mitochondrial gene, resulting in eight new sequences for three species of the genus. Both morphological and molecular analyses revealed a new species, Kempnyia krenaki sp. nov. Its nymph and that of K. umbrina are also described. With our additions, the number of known Kempnyia species rises to 41, of which 26 have COI sequences available in GenBank. Although only 11 nymphs have been associated and described for the genus so far, as the Kempnyia sequence database continues to grow, studies associating and describing nymphs will become more common, gradually reducing the Haeckelian deficit. Full article

Barnyard grass is the most problematic weed in paddy fields in Ningxia. Its substantial morphological variation complicates both identification and control, yet the genetic diversity of barnyard grass infesting paddy fields in Ningxia has not been thoroughly studied. In this research, we analyzed the genetic diversity of 46 barnyard grass populations from Ningxia’s paddy fields based on the assessment of morphological traits, DNA barcoding, and SCoT-targeted gene markers. Nine morphological traits were quantitatively analyzed, among which three phenological traits, i.e., leaf length, stem diameter, and plant height, exhibited notable variations. Correlational analysis revealed a positive relationship between morphological traits and multi-herbicide resistance profiles. To assess genetic diversity, four DNA barcodes (ITS, psbA, matK, and trnL-F) were used, among which ITS demonstrated the strongest potential in single-gene barcoding for barnyard grass species identification. Cluster analysis based on ITS barcode sequences was performed to group the populations into five main categories. Additionally, SCoT marker analysis using six primers was performed to classify the 46 barnyard grass samples into five groups. The results showed that the predominant barnyard grass species in Ningxia were E. colona, E. crus-galli var. Formosensis, E. crusgalli, E. oryzoides, and E. crusgalli var. Zelayensis, with E. colona being the most prevalent. The differences observed between the morphological and molecular marker-based classifications were method-dependent. However, both SCoT molecular marker technology and DNA barcoding contributed to identifying the genetic diversity of barnyard grass. Taken together, our study revealed significant morphological and genetic variations among barnyard grass populations, which correlated with herbicide sensitivity in Ningxia’s paddy fields, underscoring the necessity for an integrated weed management approach to combat this troublesome weed species. Full article