scholarly journals MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)

2020 ◽  
Author(s):  
Markus A. Min ◽  
Paul H. Barber ◽  
Zachary Gold

AbstractEnvironmental DNA (eDNA) is a promising biomonitoring tool for marine ecosystems, but its effectiveness for North Pacific coastal fishes is limited by the inability of existing barcoding primers to differentiate among rockfishes in the genus Sebastes. Comprised of 110 commercially and ecologically important species, this recent radiation is exceptionally speciose, and exhibits high sequence similarity among species at standard barcoding loci. Here, we report new Sebastes-specific metabarcoding primers that target mitochondrial cytochrome B. Amongst the 110 Sebastes species, 85 unique barcodes (of which 62 are species-specific) were identified in our amplicon region based on available reference sequences. The majority of the remaining barcodes are shared by only two species. Importantly, MiSebastes yield unique barcodes for 28 of 44 commercially harvested species in California, a dramatic improvement compared to the widely employed MiFish 12S primers which only recover one of 44. Tests of these primers in an aquarium mesocosm containing 16 rockfish species confirms the utility of these new primers for eDNA metabarcoding, providing an important biomonitoring tool for these key coastal marine fishes.

2004 ◽  
Vol 72 (3) ◽  
pp. 1626-1636 ◽  
Author(s):  
Erin J. Burge ◽  
David T. Gauthier ◽  
Christopher A. Ottinger ◽  
Peter A. Van Veld

ABSTRACT In mammals, the natural resistance-associated macrophage protein 1 gene, Nramp1, plays a major role in resistance to mycobacterial infections. Chesapeake Bay striped bass (Morone saxatilis) is currently experiencing an epizootic of mycobacteriosis that threatens the health of this ecologically and economically important species. In the present study, we characterized an Nramp gene in this species and obtained evidence that there is induction following Mycobacterium exposure. The striped bass Nramp gene (MsNramp) and a 554-amino-acid sequence contain all the signal features of the Nramp family, including a topology of 12 transmembrane domains (TM), the transport protein-specific binding-protein-dependent transport system inner membrane component signature, three N-linked glycosylation sites between TM 7 and TM 8, sites of casein kinase and protein kinase C phosphorylation in the amino and carboxy termini, and a tyrosine kinase phosphorylation site between TM 6 and TM 7. Phylogenetic analysis most closely grouped MsNramp with other teleost Nramp genes and revealed high sequence similarity with mammalian Nramp2. MsNramp expression was present in all tissues assayed by reverse transcription-PCR. Within 1 day of injection of Mycobacterium marinum, MsNramp expression was highly induced (17-fold higher) in peritoneal exudate (PE) cells compared to the expression in controls. The levels of MsNramp were three- and sixfold higher on days 3 and 15, respectively. Injection of Mycobacterium shottsii resulted in two-, five-, and threefold increases in gene expression in PE cells over the time course. This report is the first report of induction of an Nramp gene by mycobacteria in a poikilothermic vertebrate.


2019 ◽  
Vol 510 ◽  
pp. 31-45 ◽  
Author(s):  
Steen Wilhelm Knudsen ◽  
Rasmus Bach Ebert ◽  
Martin Hesselsøe ◽  
Franziska Kuntke ◽  
Jakob Hassingboe ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sakshi Piplani ◽  
Puneet Kumar Singh ◽  
David A. Winkler ◽  
Nikolai Petrovsky

AbstractThe devastating impact of the COVID-19 pandemic caused by SARS–coronavirus 2 (SARS-CoV-2) has raised important questions about its origins and the mechanism of its transfer to humans. A further question was whether companion or commercial animals could act as SARS-CoV-2 vectors, with early data suggesting susceptibility is species specific. To better understand SARS-CoV-2 species susceptibility, we undertook an in silico structural homology modelling, protein–protein docking, and molecular dynamics simulation study of SARS-CoV-2 spike protein’s ability to bind angiotensin converting enzyme 2 (ACE2) from relevant species. Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested, forming the highest number of hydrogen bonds with hACE2. Interestingly, pangolin ACE2 showed the next highest binding affinity despite having a relatively low sequence homology, whereas the affinity of monkey ACE2 was much lower despite its high sequence similarity to hACE2. These differences highlight the power of a structural versus a sequence-based approach to cross-species analyses. ACE2 species in the upper half of the predicted affinity range (monkey, hamster, dog, ferret, cat) have been shown to be permissive to SARS-CoV-2 infection, supporting a correlation between binding affinity and infection susceptibility. These findings show that the earliest known SARS-CoV-2 isolates were surprisingly well adapted to bind strongly to human ACE2, helping explain its efficient human to human respiratory transmission. This study highlights how in silico structural modelling methods can be used to rapidly generate information on novel viruses to help predict their behaviour and aid in countermeasure development.


Plant Disease ◽  
2013 ◽  
Vol 97 (10) ◽  
pp. 1382-1382
Author(s):  
L. L. Duarte ◽  
Y. J. Choi ◽  
R. W. Barreto

African daisy (Gerbera jamesonii Bolus ex Hook. f.) is an important species for both the cut flower and potted plant industries worldwide (4). Since the winter of 2009, plants showing severe downy mildew symptoms have been observed in a greenhouse located in an experimental area of the Universidade Federal de Viçosa (state of Minas Gerais, Brazil). The disease appeared as ill-delimited adaxial chlorosis of lamina; tissues became yellow and then brown with age with intense blighting of leaves of entire plants, leading to their death, when untreated. Dense, whitish sporulation was observed on the lower surfaces since early stages. A representative sample was dried in a plant press and deposited in the local herbarium under accession number VIC 32070. Slides were prepared with fungal structures mounted in lactofuchsin and observed under a light microscope (Olympus BX 51). Fungus morphology: Sporangiophores hypophyllous, emerging through stomata, cylindrical, up to 650 μm long and 5 to 10 μm wide, with slightly swollen base from 6.5 to 13 μm, hyaline, aseptate, straight, with up to 6 monopodial ramifications occurring mainly at right angles, the final branch ending in 3 or 4 ultimate branchlets; sporangia globose to ovoid, from 20 to 28 μm long and 13 to 18 μm wide, hyaline, smooth. Oospores were not observed. In order to further clarify the identity of the fungus on G. jamesonii, genomic DNA was extracted directly from the plant tissue and part of cytochrome c oxidase subunit 2 was amplified with the primers COX2 (3). The generated sequence was submitted to GenBank (Accession No. KC690148) and when compared with other entries revealed a high sequence similarity (99%) with Plasmopara halstedii (Farl.) Berl. & De Toni (EU743813) from Helianthus annuus L. This was also supported by the morphological data as compared with published descriptions (2) and it was then concluded that the chromistan fungus involved in downy mildew of African daisy was P. halstedii. Two different downy mildew genera, Bremia and Plasmopara, cause downy mildew disease on G. jamesoni. Bremia lactucae has been recorded in Argentina, Brazil, Germany, and Poland (4). There is only one record of a Plasmopara on this host in the United States (1), but this is an obscure report with no identification at the species level. Although P. halstedii has been commonly recorded on numerous hosts belonging to the Asteraceae worldwide, it has never been reported on G. jamesoni. To our knowledge, this is the first report of P. halstedii on G. jamesoni in Brazil. This disease has the potential to become important and cause significant losses because of a combination of the high severity to untreated plants and the increasing importance of African daisy in the flower market in Brazil. References: (1) S. A. Alfieri, Jr. et al. Bull. 11. Index of Plant Diseases in Florida (Revised). Florida Dep. Agric. Consumer Serv., Div. Plant Ind., 1984. (2) G. Hall. Plasmopara halstedii. CMI Descriptions of Pathogenic Fungi and Bacteria No 979. Mycopathologia 106:205, 1989. (3) D. S. S. Hudspeth et al. Mycologia 92:674, 2000. (4) S. M. Wolcan, Australas. Plant Dis. Notes 5:98, 2010.


1998 ◽  
Vol 180 (6) ◽  
pp. 1431-1437 ◽  
Author(s):  
Magdalen Lindeberg ◽  
Carol M. Boyd ◽  
Noel T. Keen ◽  
Alan Collmer

ABSTRACT The type II secretion system (main terminal branch of the general secretion pathway) is used by diverse gram-negative bacteria to secrete extracellular proteins. Proteins secreted by this pathway are synthesized with an N-terminal signal peptide which is removed upon translocation across the inner membrane, but the signals which target the mature proteins for secretion across the outer membrane are unknown. The plant pathogens Erwinia chrysanthemi andErwinia carotovora secrete several isozymes of pectate lyase (Pel) by the out-encoded type II pathway. However, these two bacteria cannot secrete Pels encoded by heterologously expressed pel genes from the other species, suggesting the existence of species-specific secretion signals within these proteins. The functional cluster of E. chrysanthemi out genes carried on cosmid pCPP2006 enables Escherichia coli to secreteE. chrysanthemi, but not E. carotovora, Pels. We exploited the high sequence similarity between E. chrysanthemi PelC and E. carotovora Pel1 to construct 15 hybrid proteins in which different regions of PelC were replaced with homologous sequences from Pel1. The differential secretion of these hybrid proteins by E. coli(pCPP2006) revealed M118 to D175 and V215 to C329 as regions required for species-specific secretion of PelC. We propose that the primary targeting signal is contained within the external loops formed by G274 to C329 but is dependent on residues in M118 to D170 and V215 to G274 for proper positioning.


Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Mohamed Ramadan ◽  
Muna Alariqi ◽  
Yizan Ma ◽  
Yanlong Li ◽  
Zhenping Liu ◽  
...  

Abstract Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.


Author(s):  
Angélique Buton ◽  
Louis-Marie Bobay

Abstract Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.


Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 947-957 ◽  
Author(s):  
John G Jelesko ◽  
Kristy Carter ◽  
Whitney Thompson ◽  
Yuki Kinoshita ◽  
Wilhelm Gruissem

Abstract Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 × 10-6. A nonuniform distribution of recombination resolution sites resulted in the biased formation of recombinant RBCS3B/1B::LUC genes with nonchimeric exons. The positioning of approximately half of the mapped resolution sites was effectively modeled by the fractional length of identical DNA sequences. In contrast, the other mapped resolution sites fit an alternative model in which recombination resolution was stimulated by an abrupt transition from a region of relatively high sequence similarity to a region of low sequence similarity. Thus, unequal recombination between paralogous RBCSB genes on sister chromatids created an allelic series of novel chimeric genes that effectively resulted in the diversification rather than the homogenization of the synthRBCSB1 gene cluster.


Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1692
Author(s):  
Li Gu ◽  
Ting Su ◽  
Ming-Tai An ◽  
Guo-Xiong Hu

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.


1978 ◽  
Vol 5 (1) ◽  
pp. 23 ◽  
Author(s):  
Michael H. Horn ◽  
Larry G. Allen

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