scholarly journals Transcriptional identification of genes light-interacting in the extraretinal photoreceptors of the crayfish Procambarus clarkii

ZooKeys ◽  
2021 ◽  
Vol 1072 ◽  
pp. 107-127
Author(s):  
Gabina Calderón-Rosete ◽  
Juan Antonio González-Barrios ◽  
Celia Piña-Leyva ◽  
Hayde Nallely Moreno-Sandoval ◽  
Manuel Lara-Lozano ◽  
...  
Keyword(s):  
Nerve Cord ◽  
Procambarus Clarkii ◽  
Gene Families ◽  
Illumina Miseq ◽  
Transcriptome Data ◽  
Environmental Lighting ◽  
Molecular Aspects ◽  
First Time ◽  
Phototransduction Cascade ◽  
Neuroendocrine Functions

Crayfish serve as a model for studying the effect of environmental lighting on locomotor activity and neuroendocrine functions. The effects of light on this organism are mediated differentially by retinal and extraretinal photoreceptors located in the cerebroid ganglion and the pleonal nerve cord. However, some molecular aspects of the phototransduction cascade in the pleonal extraretinal photoreceptors remain unknown. In this study, transcriptome data from the pleonal nerve cord of the crayfish Procambarus clarkii (Girard,1852) were analyzed to identify transcripts that potentially interact with phototransduction process. The Illumina MiSeq System and the pipeline Phylogenetically Informed Annotation (PIA) were employed, which places uncharacterized genes into pre-calculated phylogenies of gene families. Here, for the first time 62 transcripts identified from the pleonal nerve cord that are related to light-interacting pathways are reported; they can be classified into the following 11 sets: 1) retinoid pathway in vertebrates and invertebrates, 2) photoreceptor specification, 3) rhabdomeric phototransduction, 4) opsins 5) ciliary phototransduction, 6) melanin synthesis, 7) pterin synthesis, 8) ommochrome synthesis, 9) heme synthesis, 10) diurnal clock, and 11) crystallins. Moreover, this analysis comparing the sequences located on the pleonal nerve cord to eyestalk sequences reported in other studies reveals 94–100% similarity between the 55 common proteins identified. These results show that both retinal and pleonal non-visual photoreceptors in the crayfish equally expressed the transcripts involved in light detection. Moreover, they suggest that the genes related to ocular and extraocular light perception in the crayfish P. clarkii use biosynthesis pathways and phototransduction cascades commons.

scholarly journals Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3955 ◽  
Author(s):  
Yiling Niu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingfu Li
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Families ◽  
Shoot Meristem ◽  
Axillary Shoot ◽  
Multiple Sequence ◽  
Genome Wide ◽  
First Time

Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.

scholarly journals Detection and monitoring of insect traces in bioaerosols

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10862
Author(s):  
Panyapon Pumkaeo ◽  
Junko Takahashi ◽  
Hitoshi Iwahashi
Keyword(s):  
Aerosol Particles ◽  
Illumina Miseq ◽  
Identification Accuracy ◽  
Insect Community ◽  
Cytochrome C Oxidase I ◽  
True Bugs ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Pm2.5 And Pm10 ◽  
First Time

Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results.

scholarly journals Identification of arbuscular mycorrhizal fungi in soils of the North Caucasus based on Illumina MiSeq data for ITS1 and ITS2 regions

2020 ◽  
Vol 23 ◽  
pp. 02013
Author(s):  
Andrey P. Yurkov ◽  
Alexey A. Kryukov ◽  
Anastasia O. Gorbunova ◽  
Andrey V. Shcherbakov ◽  
Peter M. Zhurbenko
Keyword(s):  
Sample Preparation ◽  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Illumina Miseq ◽  
North Caucasus ◽  
Operational Taxonomic Units ◽  
The North ◽  
First Time ◽  
Its1 And Its2

The objective of our research was to analyze the efficiency of identification of arbuscular mycorrhizal fungi (AMF) for 2 regions: ITS1 and ITS2 regions of AMF DNA isolated from the soils of the North Caucasus (Karachay-Cherkessia). For the first time the necessity of different AMF species identification using both ITS regions was revealed, but not one region. The research demonstrated: 1) the set of taxa is different using ITS1- and ITS2-based identification; 2) analysis of the ITS1 region reveals a greater number of operational taxonomic units; 3) ITS2 allows identification of AMF at the species level more often. Sample preparation for Illumina MiSeq analysis was optimized. Obligatory stages in the sample preparation were the purification of DNA in the agarose gel in Silica after isolation, as well as separate amplification of ITS1 and ITS2 followed by combining and joint sequencing for each sample. The results showed the highest AMF biodiversity for the 176Te sample from the ecosystem of the subalpine meadow of the southeastern slope of Malaya Hatipara mountain (43°25′48.0″N 41°42′31.0″E; 2401 m above sea level), in which 8 species of AMF were identified (Archaeospora spainiae, Claroideoglomus claroideum, Diversispora versiformis, Entrophpora infrequens, Funneliformis mosseae, Glomus indicum, Paraglomus laccatum, Rhizophagus irregularis).

scholarly journals Brought more than twice: the complex introduction history of the red swamp crayfish into Europe

2019 ◽  
pp. 2 ◽  
Author(s):  
Francisco J. Oficialdegui ◽  
Marta I. Sánchez ◽  
Christophe Lejeusne ◽  
Nic Pacini ◽  
Miguel Clavero
Keyword(s):  
Western Europe ◽  
Procambarus Clarkii ◽  
Western United States ◽  
Lake Naivasha ◽  
Wild Populations ◽  
Pet Trade ◽  
Introduction History ◽  
Red Swamp Crayfish ◽  
History Of ◽  
First Time

One of the biggest challenges in understanding and managing biological invasions is the identification of the routes of introduction. This information is often incomplete because of unnoticed, unreported and, sometimes, illegal translocations. Reports on the introduction of the red swamp crayfish (Procambarus clarkii) into Europe describe that it was introduced for the first time to southern Spain (1973 and 1974) from Louisiana; from there, it rapidly spread throughout several European countries. While other importation events and pathways of introduction have been suggested in the literature, there is no evidence that these led to wild populations in Europe. Our present study suggests two additional introduction routes into Europe from non-European areas where the red swamp crayfish had previously been reported. By using mtDNA, we found a shared haplotype between the Lake Naivasha in Kenya and Western Europe, as well as another between either western United States or Asia, and Malta. These findings support historical reports found in the literature for the former case and also point towards pet trade as driver of new introductions for the latter, thus highlighting the complex introduction history of the red swamp crayfish populations in Europe.

scholarly journals The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection

Gut ◽  
2016 ◽  
Vol 67 (2) ◽  
pp. 216-225 ◽  
Author(s):  
Christian Schulz ◽  
Kerstin Schütte ◽  
Nadine Koch ◽  
Ramiro Vilchez-Vargas ◽  
Melissa L Wos-Oxley ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Illumina Miseq ◽  
Gi Tract ◽  
Upper Gi ◽  
Miseq Platform ◽  
H Pylori ◽  
Bacterial Assemblages ◽  
First Time ◽  
Upper Gi Tract

ObjectivePatients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches.DesignSaliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1–V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform.ResultsOverall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components. Helicobacter spp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities.ConclusionsThe detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence of Helicobacter spp on the global community structures is striking.

scholarly journals Habitat use and population structure of the invasive red swamp crayfish Procambarus clarkii (Girard, 1852) in a protected area in northern Italy

2018 ◽  
pp. 12 ◽  
Author(s):  
Roberta Donato ◽  
Marta Rollandin ◽  
Livio Favaro ◽  
Alessio Ferrarese ◽  
Daniela Pessani ◽  
...  
Keyword(s):  
Riparian Vegetation ◽  
Life History Traits ◽  
Invasive Alien Species ◽  
Procambarus Clarkii ◽  
Condition Index ◽  
Sampling Effort ◽  
Red Swamp Crayfish ◽  
Crayfish Population ◽  
One Year ◽  
First Time

The red swamp crayfish Procambarus clarkii is one of the most invasive alien species in Europe and included in the list of invasive species of Union concern. We describe for the first time some life-history traits of a red swamp crayfish population in the Nature Reserve of the Lago di Candia (Italy). We investigated (1) preferences of this species for specific environmental features on the banks of the lake, and (2) differences in size, sex ratio, and condition index between individuals caught in lake and marsh. Moreover, we compared sampling effort and the features of individuals caught in the lake, for two sampling seasons in 2014 and 2015. Findings indicated that the population was well established, and the marsh seemed to have better conditions for growth of individuals than the lake. Accordingly, continuity of riparian vegetation, opportunity to dig burrows, and trophic resource availability seems to facilitate the proliferation of the crayfish in the lake. Our study demonstrated that massive removal efforts over the whole active period of the species and more than one year of trapping are necessary to increase the controlling activities' success. This study could have important implications for further population management projects directed at biodiversity conservation in the area.

scholarly journals Tarantula phylogenomics: A robust phylogeny of multiple tarantula lineages inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution

2018 ◽  
Author(s):  
Stephen Foley ◽  
Tim Lueddecke ◽  
Dong-Qiang Chen ◽  
Henrik Krehenwinkel ◽  
Sven Kuenzel ◽  
...  
Keyword(s):  
New World ◽  
Strong Support ◽  
Morphological Data ◽  
Ancestral State ◽  
Transcriptome Data ◽  
Large Size ◽  
The Family ◽  
History Of ◽  
Almost All ◽  
First Time

Mygalomorph spiders of the family Theraphosidae, known to the broader public as tarantulas, are among the most recognizable arachnids on earth due to their large size and widespread distribution. Their use of urticating setae is a notable adaptation that has evolved exclusively in certain New World theraphosids. Thus far, the evolutionary history of Theraphosidae remains poorly understood; theraphosid systematics still largely relies on morphological datasets, which suffer from high degrees of homoplasy, and traditional targeted sequencing of preselected genes failed to provide strong support for supra-generic clades (i.e. particularly those broader than subfamilies). In this study, we provide the first robust phylogenetic hypothesis of theraphosid evolution inferred from transcriptome data. A core ortholog approach was used to generate a phylogeny from 2460 orthologous genes across 25 theraphosid genera, representing all of the major theraphosid subfamilies, except Selenogyrinae. For the first time our phylogeny recovers a monophyletic group that comprises the vast majority of New World theraphosid subfamilies including Aviculariinae and Theraphosinae. Concurrently, we provide additional evidence for the integrity of questionable subfamilies, such as Poecilotheriinae and Psalmopoeinae, and support the non-monophyly of Ischnocolinae. The deeper relationships between almost all subfamilies are confidently inferred for the first time. We also used our phylogeny in tandem with published morphological data to perform ancestral state analyses on urticating setae. This revealed that the evolution of this important defensive trait might be explained by three equally parsimonious scenarios.

scholarly journals Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq

2021 ◽  
Vol 10 (4) ◽  
Author(s):  
Nihad A. M. Al-Rashedi ◽  
Danilo Licastro ◽  
Sreejith Rajasekharan ◽  
Simeone Dal Monego ◽  
Alessandro Marcello ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Illumina Miseq ◽  
Spike Protein ◽  
Protein Coding ◽  
Novel Coronavirus ◽  
First Time

ABSTRACT The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq.

scholarly journals The First Whole Genome Sequencing of Sanghuangporus sanghuang Provides Insights into Its Medicinal Application and Evolution

2021 ◽  
Vol 7 (10) ◽  
pp. 787
Author(s):  
Ji-Hang Jiang ◽  
Sheng-Hua Wu ◽  
Li-Wei Zhou
Keyword(s):  
Genome Sequencing ◽  
Genome Sequence ◽  
Gene Families ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Nutritional Strategy ◽  
Ancient People ◽  
Medicinal Properties ◽  
Comparative Genomics Analysis ◽  
First Time

Sanghuangporus is a medicinal macrofungal genus typified by S. sanghuang, the very species utilized in traditional Chinese medicines by Chinese ancient people. To facilitate the medicinal application of S. sanghuang, we, for the first time, perform its genome sequencing and analyses from a monokaryon strain. A 33.34 Mb genome sequence was assembled to 26 contigs, which lead to the prediction of 8278 protein-coding genes. From these genes, the potential biosynthesis pathway of sesquiterpenoids was, for the first time, identified from Sanghuangporus, besides that of triterpenoids. While polysaccharides are the main medicinal metabolites in S. sanghuang, flavonoids are especially abundant medicinal metabolites comparing with other medicinal macrofungal groups. From the genomic perspective, S. sanghuang has a tetrapolar heterothallic mating system, and has its special nutritional strategy and advantageous medicinal properties compared with S. baumii and S. vaninii. A phylogenomics analysis indicates that Sanghuangporus emerged 15.39 million years ago and S. sanghuang has a closer phylogenetic relationship with S. baumii than S. vaninii. However, S. sanghuang shares a higher region of synteny and more orthologous genes, including carbohydrate-active enzymes with S. vaninii than S. baumii. A comparative genomics analysis with S. baumii and S. vaninii indicates that species diversification within Sanghuangporus may be driven by the translocation and translocation plus inversion of genome sequences, while the expansion and contraction of gene families may contribute to the host specificity of Sanghuangporus species. In general, the genome sequence of S. sanghuang provides insights into its medicinal application and evolution.

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