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04:28 EDT 23rd October 2019 | BioPortfolio

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Showing "draft genome assembly halophyte Suaeda aralocaspica plant that" PubMed Articles 1–25 of 9,800+

A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C4 photosynthesis within individual cells.

The halophyte Suaeda aralocaspica performs complete C4 photosynthesis within individual cells (SCC4), which is distinct from typical C4 plants, which require the collaboration of 2 types of photosynthetic cells. However, despite SCC4 plants having features that are valuable in engineering higher photosynthetic efficiencies in agriculturally important C3 species such as rice, there are no reported sequenced SCC4 plant genomes, limiting our understanding of the mechanisms involved in, and evolution of, SCC4 p...

The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley.

Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (H. vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high-quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36,395 high-confidence protein coding genes. BUSCO analysis revealed that the assembly included...

Draft assembly of Phytopthora capsici from long-read sequencing uncovers complexity.

Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as host and fungicide, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits wide-spread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here we leverage Oxford Nanopore Tech...

An improved genome assembly of the fluke Schistosoma japonicum.

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.

New high-quality draft genome of the brown rot fungal pathogen Monilinia fructicola.

Brown rot is a worldwide fungal disease of stone and pome fruit that is caused by several Monilinia species. Among these, Monilinia fructicola can cause severe preharvest and postharvest losses, especially for stone fruit. Here, we present a high-quality draft genome assembly of M. fructicola Mfrc123 strain obtained using both Illumina and PacBio sequencing technologies. The genome assembly comprised 20 scaffolds, including 29 telomere sequences at both ends of 10 scaffolds, and at a single end of nine scaf...

Genome Sequence Resource of the Wide-host-range Anthracnose Pathogen Colletotrichum siamense.

Colletotrichum siamense causes fruit or/and foliar disease called anthracnose on a variety of plant hosts including vegetables, fruits, ornamental plants and others, such as chili pepper, apple, American cranberry, mango, orange, papaya, guava, rubber plant, jasmine, coffee berry and tea plants. Here, we report the first Illumina-sequenced draft genome assembly of C. siamense strain ICMP 18578 and its annotation. This genome sequence provides a unique resource that will be useful for future research on the ...

A chromosome-level draft genome of the grain aphid Sitobion miscanthi.

Sitobion miscanthi is an ideal model for studying host plant specificity, parthenogenesis-based phenotypic plasticity, and interactions between insects and other species of various trophic levels, such as viruses, bacteria, plants, and natural enemies. However, the genome information for this species has not yet to be sequenced and published. Here, we analyzed the entire genome of a parthenogenetic female aphid colony using Pacific Biosciences long-read sequencing and Hi-C data to generate chromosome-length...

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa.

Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data...

A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).

Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential.

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and...

Draft Genome Sequences of Elsinoë fawcettii and Elsinoë australis causing scab diseases on citrus.

Elsinoë fawcettii and E. australis (phylum Ascomycota) are phytopathogenic fungi causing scab diseases on citrus plants. We report here the high quality draft genome sequences and ab initio gene predictions of two Elsinoë fawcettii strains and one Elsinoë australis strain, which differ in their host range. These genome sequence information will provide valuable resources to underpin genomic attributes for determining host range through comparative genomic analyses of citrus scab fungi.

A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana.

Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect.

Comparative Analysis of Draft Genome Sequence of Rhodococcus sp. Eu-32 with Other Rhodococcus Species for Its Taxonomic Status and Sulfur Metabolism Potential.

Rhodococcus sp. Eu-32 has shown an extended novel dibenzothiophene desulfurization sulfur-specific 4S pathway and could remove significant amounts of organic sulfur from coal. Here, we present the draft genome sequence of Eu-32 with a genome size of approximately 5.61 Mb, containing 5065 protein coding sequences with a G+C content of 65.1%. The Rhodococcus sp. Eu-32 showed ~ 99% identity at the 16S rRNA gene sequence level while 

Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel.

Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence-absence variations (PAVs). In this study, we present the draft de novo genome assembly of 'PHJ89', an 'Oh43'-type inbred line of maize ( L.). From three separate reference genome assemblies ('B73', 'PH207', and PHJ89) that represent the predominant germplasm groups of ma...

Genome sequence resource for Stemphylium vesicarium, causing Brown Spot Disease of Pear.

Stemphylium vesicarium is the causal agent of several plant diseases as well Brown Spot of Pear (BSP), which is one of the most economically important fungal diseases in European pear-production areas. In addition to the relevance of the economic impact, conidia widespread from plant material infected by the pathogen can trigger respiratory allergy. Here, we report the first genome of a S. vesicarium strain, the 173-1a13FI1M3, isolated from pear and sensitive to the mostly used fungicide classes currently a...

The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates.

We present the draft genome sequence of Dysdera silvatica, a nocturnal ground-dwelling spider from a genus that has undergone a remarkable adaptive radiation in the Canary Islands.

The Draft Genome Sequence of Pseudomonas putida Strain TGRB4, an Aerobic Bacterium Capable of Producing Methylmercury.

Mercury (Hg) methylation is mainly a microbial process mediated by anaerobes. The continued study of Pseudomonas putida (P. putida) strain TGRB4 genome was inspired by the fact that it can transform Hg into the highly toxic methylmercury (MeHg) under aerobic conditions. P. putida strain TGRB4 is a Gram-negative rod-shaped Gamma-proteobacterium (γ-proteobacterium), isolated from the soil in a typical water level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR), which suffered from seasonally wate...

Genome of the parasitoid wasp Diachasma alloeum, an emerging model for ecological speciation and transitions to asexual reproduction.

Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae) and a developing model for understanding how ecological speciation can "cascade" across trophic levels. Identification of gene content confirmed the overall quality of the draft genome, and we manually annotated ∼400 ...

Draft genome sequence of a clinical Acinetobacter baumannii isolate of new sequence type ST1688 from Saudi Arabia.

Acinetobacter baumannii has emerged as a most prevalent multidrug-resistant nosocomial pathogen worldwide. In this study, we report the draft genome sequence of A. baumannii strain Ab174 isolated from a neonatal patient diagnosed with acute peritonitis.

Purification of an acidic polysaccharide from Suaeda salsa plant and its anti-tumor activity by activating mitochondrial pathway in MCF-7 cells.

Suaeda salsa, is an annual herbaceous plant that contains various bio-functional macromolecules. Herein, an acidic polysaccharide from Suaeda salsa, denoted as SSP2-2, with a molecular weight of 53.8 kDa was isolated, which composed of mannose, rhamnose, glucuronic acid, galacturonic acid, galactose and xylose in a molar ratio of 0.6: 8.0: 1.0: 83.6: 5.0: 7.2. An MTT assay showed that SSP2-2 induced apoptosis of MCF-7 cells in a dose-dependent manner in vitro. Morphological analysis and flow cytometry exp...

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing.

The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford Nanopore technology (ONT).

Long-read Nanopore Sequencing-based Draft Genome of a Carbapenem-resistant Pseudomonas aeruginosa.

Pseudomonas aeruginosa (P. aeruginosa) is a common Gram-negative bacterium that can cause a series of serious infections, such as lower respiratory tract infection, urinary-tract infections with catheterized patients. Here we reported the draft genome of carbapenem-resistant P. aeruginosa.

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication.

Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world's most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing select BACs from a kochia bacte...

A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis.

Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.

Transcriptome sequencing revealed molecular mechanisms underlying tolerance of Suaeda salsa to saline stress.

The halophyte Suaeda salsa displayed strong resistance to salinity. Up to date, molecular mechanisms underlying tolerance of S. salsa to salinity have not been well understood. In the present study, S. salsa seedlings were treated with 30‰ salinity and then leaves and roots were subjected to Illumina sequencing. Compared with the control, 68,599 and 77,250 unigenes were significantly differentially expressed in leaves and roots in saline treatment, respectively. KEGG enrichment analyses indicated that pho...

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