rdna sequences
Recently Published Documents


TOTAL DOCUMENTS

1289
(FIVE YEARS 241)

H-INDEX

85
(FIVE YEARS 4)

2022 ◽  
Author(s):  
Sagheer Atta

Citrus is a valuable crop in Pakistan because it is rich in vitamin C and antioxidants. Huanglongbing (HLB) has an influence on citrus production around the world caused by a bacterium “ Candidatus   liberibacter asiaticus ” (CLas), africanus and americanus. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit,  Citrus aurantifolia , and  Citrus reticulata  Blanco was used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5–V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria.  Citrus aurantifolia  and  Citrus paradisi  showed almost equal diversity, whereas  Citrus reticulata  Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.


Botany ◽  
2022 ◽  
Author(s):  
Rosario Gregorio-Cipriano ◽  
Dolores González ◽  
Rubén Félix-Gastélum ◽  
Santiago Chacón

Powdery mildew is one of the most severe diseases affecting Cucurbitaceae. We identify the members of Erysiphaceae infecting cucurbits in three producing regions in Mexico. We determined that Golovinomyces ambrosiae, Neoerysiphe sechii, and Podosphaera xanthii infected cultivated and wild cucurbits species or subspecies. Leaf samples showing symptoms and signs of powdery mildew were collected from the northwestern, central western, and eastern regions of Mexico between 2017 and 2020. Species associated with the disease were identified based on morphology and ITS rDNA sequences. All powdery mildew specimens presented only the anamorph. Podosphaera xanthii was the predominant species; it was found in 85.7 % of the samples and in 13 out of 14 species or subspecies of cucurbits. Neoerysiphe sechii was found in 15.23 % of the samples and in only four cucurbit species from the central western and eastern regions of Mexico. Golovinomyces ambrosiae was documented for the first time in a Cucurbitaceae species (Sicyos deppei) from Central West Mexico. Three new hosts were registered for Neoerysiphe sechii (Cucurbita ficifolia, Echinopepon milleflorus, and Sicyos laciniatus) and eight for Podosphaera xanthii (Cucurbita argyrosperma, C. argyrosperma subsp. sororia, C. ficifolia, C. okeechobeensis subsp. martinezii, C. radicans, Sechium edule, Sicyos laciniatus, and S. deppei).


2022 ◽  
Author(s):  
Jing Feng ◽  
Shu-Yan Liu ◽  
Uwe Braun ◽  
Susumu Takamatsu ◽  
Michael Bradshaw ◽  
...  

Abstract Recently performed phylogenetic-taxonomic analyses of species belonging to Erysiphe sect. Uncinula on willows (Salix spp.) demonstrated a much higher diversity than previously assumed. Phylogenetic analyses and morphological examinations of Chinese Erysiphe collections on Salix abscondita (= S. raddeana), S. sinica and S. taraikensis, all belonging to Salix subgen. Vetrix sect. Vetrix, revealed an additional cryptic species in sister position to the E. salicis clade, which is described as Erysiphe salicina. The new species clearly distinguished from all allied species in morphological and genetical results. The phylogeny of the new species and closely related species on Populus and Salix spp. (Salicaceae) was reconstructed and discussed using a combined alignment of the internal transcribed spacer (ITS) regions and 28S rDNA sequences. The present phylogenetic analyses suggest that the recently described E. salicicola (on Salix gracilistyla in South Korea) has to be reduced to synonymy with E. salicis var. salicis-gracilistylae (º Uncinula salicis-gracilistylae).


ZooKeys ◽  
2021 ◽  
Vol 1079 ◽  
pp. 145-227
Author(s):  
Karl J. Wittmann ◽  
Pierre Chevaldonné

SCUBA diving explorations of three islands off Dumont d’Urville Station at the coast of Adélie Land, East Antarctica, enabled the observation of marine ice caves. Sampling in this unusual habitat yielded a total of three species of Mysidae, altogether previously poorly known or unknown to science. Pseudomma kryotroglodytumsp. nov. is described, based on the structure of the antennal scale, telson and on cornea-like lateral portions set off against the main body of eyeplates. Mysidetes illigi is re-established at species level after almost a century in synonymy. Re-descriptions are provided for M. illigi and M. hanseni, based on types and ice cave materials. Keys to the Southern Ocean species of Pseudomma and to the world-wide species of Mysidetes are given. Phylogenetic trees are provided for the genera Pseudomma and Mysidetes. 18S rDNA sequences of P. kryotroglodytum differ from GenBank sequences of other Pseudomma species. First sequence data are given for species of the genus Mysidetes: 18S differs between the two examined species and COI is quite diverse between and within species. We found previously unknown, probably sensorial structures in these ice cave species: in P. kryotroglodytum, the basal segment of the antennula shows a pit-like depression with striated pad on the bottom and a median cyst, connected with the bottom of the eyeplate cleft. M. illigi shows a female homologue of the appendix masculina bearing a field of modified setae. Subsequent investigations demonstrated these structures also in species from other habitats. The feeding apparatus and stomach contents of the three ice cave species point to brushing of small particles (detritus, microalgae) from available surfaces, such as sediment, rock and the ice surface. Differences in the feeding apparatus are very subtle between the two Mysidetes species. The high content of fat bodies in M. hanseni could help it to survive periods of starvation. The large storage volume of the foregut in P. kryotroglodytum points to the collection of food with low nutritional quality and could help to balance strongly fluctuating food availability. Summer specimens of M. hanseni showed a bimodal frequency of developmental stages in the marsupium and bimodal size-frequency distribution of free-living stages. The females with younger brood (embryos) were, on average, larger and carried more marsupial young than those with older brood (nauplioid larvae). All examined incubating and spent females showed (almost) empty foreguts and empty ovarian tubes, suggesting possible semelparity and death following the release of young. The absence of juveniles and immature females from summer samples suggests that growth and accumulation of fat and yolk occur outside ice caves, while such caves could be used by fattened adults as shelter for brooding. A provisional interpretation proposes a biannual life cycle for M. hanseni, superimposed with shifted breeding schedules, the latter characterised by early breeding and late breeding females, probably in response to harsh physical and trophic conditions along the continental coast of Antarctica.


Author(s):  
Lixia Shang ◽  
Xinyu Zhai ◽  
Wen Tian ◽  
Yuyang Liu ◽  
Yangchun Han ◽  
...  

Over the past several decades, much attention has been focused on the dispersal of aquatic nonindigenous species via ballast tanks of shipping vessels worldwide. The recently reclassified dinoflagellate Pseudocochlodinium profundisulcus (previously identified as Cochlodinium sp., Cochlodinium geminatum, or Polykrikos geminatus) was not reported in China until 2006. However, algal blooming events caused by this organism have been reported almost every year since then in the Pearl River Estuary and its adjacent areas in China. Whether P. profundisulcus is an indigenous or an invasive species has thus become an ecological question of great scientific and practical significance. In this study, we collected the sediments from ballast tanks of ships arriving in the ports of China and North America and characterized dinoflagellate resting cysts via a combined approach. We germinated two dark brownish cysts from the tank of an international ship (Vessel A) arriving at the Jiangyin Port (China) into vegetative cells and identified them as P. profundisulcus by light and scanning electron microscopy and phylogenetic analyses for partial LSU rDNA sequences. We also identified P. profundisulcus cyst from the ballast tank sediment of a ship (Vessel B) arriving in the port of North America via single-cyst PCR and cloning sequencing, which indicated that this species could be transported as resting cyst via ship. Since phylogenetic analyses based on partial LSU rDNA sequences could not differentiate all sequences among our cysts from those deposited in the NCBI database into sub-groups, all populations from China, Australia, Japan, and the original sources from which the cysts in the two vessels arrived in China and North America were carried over appeared to share a very recent common ancestor, and the species may have experienced a worldwide expansion recently. These results indicate that P. profundisulcus cysts may have been extensively transferred to many regions of the world via ships’ ballast tank sediments. While our work provides an exemplary case for both the feasibility and complexity (in tracking the source) of the bio-invasion risk via the transport of live resting cysts by ship’s ballast tanks, it also points out an orientation for future investigation.


Author(s):  
Rickard Westerman ◽  
Mohammed Ahmed ◽  
Oleksandr Holovachov

AbstractTwo new species of nematodes associated with crabs are described from New Caledonia. Gammarinema scyllaesp. n. from the gill chambers of Scylla serrata (Forsskål) is characterised by 3–4 mm long body, small outer labial and cephalic sensilla, distinct ocelli, short straight spicules and sub-cylindrical tail. Monhystrium mangrovisp. n. from the gill chambers and body cavity of mangrove crab Neosarmatium sp. is characterised by 1–1.4 mm long body; outer labial sensilla longer than cephalic sensilla, amphid located at level with posterior stoma chamber, denticles in posterior stoma chamber and five pairs of genital papilla on tail. Phylogenetic relationships of two new species and other nematodes from the family Monhysteridae are analysed based on 18S and partial 28S rDNA sequences.


2021 ◽  
Vol 15 (4) ◽  
pp. 507-525
Author(s):  
Alessio Turco ◽  
Antonella Albano ◽  
Pietro Medagli ◽  
Robert P. Wagensommer ◽  
Saverio D'Emerico

In our study, FISH mapping using 18S-5.8S-25S rDNA and 5S rDNA sequences was performed for the first time on Ophrys tenthredinifera Willdenow, 1805, Serapias vomeracea (Burman f., 1770) Briquet, 1910 and Himantoglossum hircinum (Linnaeus, 1753) Sprengel, 1826. A detailed study was also performed on O. tenthredinifera using Giemsa-staining, silver-staining, CMA fluorescence banding and fluorescence in situ hybridisation (FISH) with rDNA probes. We analysed two subspecies, i.e. O. tenthredinifera subsp. neglecta (Parlatore, 1860) E.G. Camus, 1908 and O. tenthredinifera subsp. grandiflora (Tenore, 1819) Kreutz, 2004 by the traditional Feulgen method and constructed the karyotype. The cytotaxonomic implications for both taxa are also discussed. In Himantoglossum hircinum, FISH and silver staining highlighted differences in the number of two rDNA families (35S and 5S) with respect to Barlia robertiana (Loiseleur-Deslongchamps, 1807) Greuter, 1967. In addition, fluorescence in situ hybridisation was also applied to diploid (2n = 2x = 36) and triploid (2n = 3x = 54) Anacamptis morio (Linnaeus, 1753) R.M. Bateman, Pridgeon et M.W. Chase, 1997. As far as we are aware, this is the first case of autotriploidy observed in A. morio.


2021 ◽  
Author(s):  
Mitsunori Iwataki ◽  
Wai Mun Lum ◽  
Koyo Kuwata ◽  
Kazuya Takahashi ◽  
Daichi Arima ◽  
...  

Harmful algal blooms responsible for mass mortalities of marine organisms have so far been rare in Hokkaido, northern Japan, although fish killing blooms have been frequently reported from western Japanese coasts. In September–November 2021, a huge and prolonged cold-water bloom occurred along the Pacific coast of eastern Hokkaido, Japan, and was associated with intensive mortalities of sea urchin, fish, octopus, shellfish, etc. In this study, morphology and phylogeny of the dominant and co-occurred unarmored dinoflagellates of the Kareniaceae in the bloom were examined by using light microscopy, scanning electron microscopy and molecular phylogeny inferred from ITS and LSU rDNA (D1–D3) sequences. Morphological observation and molecular phylogeny showed that the dominant species was Karenia selliformis, with co-occurrences of other kareniacean dinoflagellates, Kr. longicanalis, Kr. mikimotoi, Karlodinium sp., Takayama cf. acrotrocha, Takayama tuberculata and Takayama sp. The typical cell forms of K. selliformis in the bloom were discoid, dorsoventrally flattened, and larger than the cell sizes in previous reports, 35.3–43.6 (39.4±2.1) µm in length. Transparent cells of Kr. selliformis lacking or having several shrunken chloroplasts and oil droplets were also found. Cells of Kr. selliformis had morphological variation, but the species could be distinguished from other co-occurred Karenia species by its numerous (46–105) and small granular (2.9–4.6 µm in diameter) chloroplasts and the nucleus positioned in the hypocone. Cell density of Kr. selliformis exceeding 100 cells/mL was recorded in the range of temperature 9.8–17.6°C. The rDNA sequences determined from Kr. selliformis in the blooms of Hokkaido, Japan in 2021 were identical to those from another bloom in Kamchatka, Russia in 2020.


Water ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 3581
Author(s):  
Vasco Menconi ◽  
Perla Tedesco ◽  
Paolo Pastorino ◽  
Ivano Confortini ◽  
Giuseppe Esposito ◽  
...  

The nematode Eustrongylides excisus is a parasite of freshwater fish- and fish-eating birds, with known differences on prevalence values among fish species. Thus, the present study aims to explore the hypothesis that the feeding behavior and the size of fish belonging to different trophic levels could explain such differences. For that, 14 sampling sites were selected to perform a fish parasitological survey on Lake Garda (Italy) during spring-summer 2020. Amplification of nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences of nematodes morphologically ascribable to the genus Eustrongylides allowed to identify them as E. excisus. From the five studied fish species (Perca fluviatilis, Lepomis gibbous, Coregonus lavaretus, Alosa fallax lacustris and Micropterus salmoides), only three presented the parasite E. excisus: P. fluviatilis, L. gibbous and M. salmoides, with significant differences in prevalence values among species (p = 0.002). Additionally, there were differences in prevalence values within the same fish species captured from different sampling sites. Findings showed that mainly piscivorous fish were positive for E. excisus and how the prevalence was highest in M. salmoides. As regard the fish size, a negative correlation between body size and E. excisus was found in P. fluviatilis due to the feeding habit of juvenile perch which feed mainly zooplankton and benthic invertebrates (i.e., oligochaetes, which are the first intermediate hosts of E. excisus). The study findings advance novel knowledge in the field of pathogens of zoonotic importance in the aquatic environment.


2021 ◽  
Vol 12 ◽  
Author(s):  
Mingzhen Ma ◽  
Yuqing Li ◽  
Qingxiang Yuan ◽  
Xuetong Zhao ◽  
Khaled A. S. Al-Rasheid ◽  
...  

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna, while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya, was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya, still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.


Sign in / Sign up

Export Citation Format

Share Document