draft genome
Recently Published Documents


TOTAL DOCUMENTS

6837
(FIVE YEARS 2190)

H-INDEX

70
(FIVE YEARS 11)

2022 ◽  
Vol 18 (1) ◽  
pp. 1-13
Author(s):  
Ramanathan Sowdhamini ◽  

Saffron (Crocus sativus L.) is the low yielding plant of medicinal and economic importance. Therefore, it is of interest to report the draft genome sequence of C. sativus. The draft genome of C. sativus has been assembled using Illumina sequencing and is 3.01 Gb long covering 84.24% of genome. C. sativus genome annotation identified 53,546 functional genes (including 5726 transcription factors), 862,275 repeats and 964,231 SSR markers. The genes involved in the apocarotenoids biosynthesis pathway (crocin, crocetin, picrocrocin, and safranal) were found in the draft genome analysis.


Author(s):  
Rei-Hsing Hu ◽  
Chia-Ta Wu ◽  
Ting-Shuan Wu ◽  
Feng-Yih Yu ◽  
Jiunn-Liang Ko ◽  
...  

BackgroundAllergic asthma, a chronic airway inflammatory disease, is a critical public health problem. Indoor house dust mites (HDMs) could cause allergic asthma. The prevalence of sensitization to Dermatophagoides microceras (Der m) was approximately 80% and is related to the immunoglobulin E crossing-reactivity of mites belonging to the same genus, Dermatophagoides pteronyssinus (Der p) and Dermatophagoides farina (Der f). However, studies on Der m are scant.MethodsWe used integrated OMICs approaches to identify and characterize the group 2 mite allergen-like protein in Der m (Der m 2). We established a Der m 2-induced allergic asthma mouse model and treated the mice with a fungal immunomodulatory protein (FIP-fve) isolated from Flammulina veluptipes to evaluate the allergenicity of Der m 2 and the immunomodulatory effects of FIP-fve.ResultsBy performing de novo draft genome assembly and comparative genome analysis, we identified the putative 144-amino acid Der m 2 in silico and further confirmed its existence through liquid chromatography–tandem mass spectrometry. Der m 2 is a lipopolysaccharides (LPS)-binding protein. Thus, we examined the LPS-binding activity of recombinant Der m 2 by performing molecular docking analysis, co-immunoprecipitation (Co-IP), and a pull-down assay. Der m 2 elicited the production of pro-inflammatory cytokines, interleukin (IL)-6, and IL-8 in BEAS-2B cells, a human bronchial epithelial cell line, and induced airway hyperresponsiveness in mice. Furthermore, in mice sensitized with Der m 2, the administration of FIP-fve in either the earlier stage or the late stage, FIP-fve alleviated allergic asthma by moderating airway inflammation and remodeling.ConclusionsDer m 2 induced inflammatory responses in cell and mouse models. FIP-fve alleviated inflammation in Der m 2-induced asthma in mice by exerting an immunomodulatory effect.


Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 148
Author(s):  
Clifton P. Bueno de Mesquita ◽  
Jinglie Zhou ◽  
Susanna Theroux ◽  
Susannah G. Tringe

Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that both of these metagenome-assembled genomes (MAGs) represent new species in the genus. Average nucleotide identities to the closest taxon were <85%. The MAGs were assembled with SPAdes, binned with MetaBAT, and curated with scaffold extension and reassembly. Both genomes contained the phnCDEGHIJLMP suite of genes encoding the full C-P lyase pathway of methylphosphonate degradation and were significantly more abundant in two former industrial salterns than in nearby reference and restored wetlands, which have lower salinity levels and lower methane emissions than the salterns. These organisms contain a variety of compatible solute biosynthesis and transporter genes to cope with high salinity levels but harbor only slightly acidic proteomes (mean isoelectric point of 6.48).


Author(s):  
Isabel Fuenzalida-Valdivia ◽  
Maria Victoria Gangas ◽  
Diego Zavala ◽  
Ariel Herrera-Vásquez ◽  
Fabrice Roux ◽  
...  

Here, we report the genome sequence of the P. syringae strain RAYR-BL, isolated from natural accessions of Arabidopsis plants. The draft genome sequence consists of 5.85 Mbp assembled in 110 contigs. The study of P. syringae RAYR-BL is a valuable tool to investigate molecular features of plant-pathogen interaction under environmental conditions.


Author(s):  
Tammy J. Barnaba ◽  
Jayanthi Gangiredla ◽  
Mark K. Mammel ◽  
David W. Lacher ◽  
Carmen Tartera

We present the genome sequences of nine Bacillus isolates and two Weizmannia isolates from 10 different dietary supplements and one cultured food product. Strains of these species have been associated with health benefits when ingested by humans, due to their ability to survive the stomach’s acidic environment and colonize the intestinal tract.


Author(s):  
Kyosuke Yamamoto ◽  
Yasuko Yoneda ◽  
Ayaka Makino ◽  
Yasuhiro Tanaka ◽  
Xian-Ying Meng ◽  
...  

Here, we report a draft genome sequence of a bacterial strain, F-183, isolated from a duckweed frond. Strain F-183 belongs to the family Bryobacteraceae of the phylum Acidobacteria , and its genomic information would contribute to understanding the ecophysiology of this abundant but rarely characterized phylum.


Author(s):  
Tomijiro Hara ◽  
Yumiko Takatsuka ◽  
Yuh Shiwa ◽  
Kenji Yokota

We report a draft genome sequence of Comamonas testosteroni strain YAZ2, a polychlorinated biphenyl (PCB) degrader that was isolated from a PCB-unpolluted environment. The assembled genome contains a single 5.4-Mb chromosome and an 87-kb plasmid. The bph gene cluster, which is involved in PCB degradation, was found on the chromosome.


2022 ◽  
Author(s):  
Takanori Yamashiro ◽  
Akira Shiraishi ◽  
Koji Nakayama ◽  
Honoo Satake

Abstract The plant Tanacetum coccineum (painted daisy) is closely related to Tanacetum cinerariifolium (pyrethrum daisy). However, T. cinerariifolium produces large amounts of pyrethrins, a class of natural insecticides, whereas T. coccineum produces much smaller amounts of these compounds. Thus, comparative genomic analysis is expected to contribute a great deal to investigating the difference in biological defense systems, including pyrethrin biosynthesis. Here, we elucidated the 9.4-Gb draft genome of T. coccineum, consisting of 2,836,647 scaffolds and 103,680 genes. Comparative analyses of the draft genome of T. coccineum and that of T. cinerariifolium, generated in our previous study, revealed distinct features of T. coccineum genes. While the T. coccineum genome contains more numerous ribosome-inactivating protein (RIP)-encoding genes, the number of higher-toxicity type-II RIP-encoding genes is larger in T. cinerariifolium. Furthermore, the number of histidine kinases encoded by the T. coccineum genome is smaller than that of T. cinerariifolium, suggesting a biological correlation with pyrethrin biosynthesis. Moreover, the flanking regions of pyrethrin biosynthesis-related genes are also distinct between these two plants. These results provide clues to elucidation of species-specific biodefense systems, including the regulatory mechanisms underlying pyrethrin production.


Author(s):  
Hend Altaib ◽  
Ryo Niwa ◽  
Mayuko Abe ◽  
Tohru Suzuki

Bifidobacterium adolescentis 4-2 was isolated from healthy human feces. Here, we report a draft genome sequence of this bacterium, which may clarify the functionality of gut microbiota-brain communication. The draft genome comprises 2.39 Mb, with an average G+C content of 59.2% and 2,028 coding DNA sequences. An operon for GABA biosynthesis was observed in the draft genome.


2022 ◽  
Author(s):  
Shinichi Morita ◽  
Tomoko F. Shibata ◽  
Tomoaki Nishiyama ◽  
Yuuki Kobayashi ◽  
Katsushi Yamaguchi ◽  
...  

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.


Sign in / Sign up

Export Citation Format

Share Document