scholarly journals The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus

2019 ◽  
Vol 11 (7) ◽  
pp. 1965-1970 ◽  
Author(s):  
Nikola Palevich ◽  
Paul H Maclean ◽  
Abdul Baten ◽  
Richard W Scott ◽  
David M Leathwick
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Sequence Data ◽  
Animal Health ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Parasitic Nematodes ◽  
Hybrid Assembly ◽  
Genetic Structures

Abstract Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.

scholarly journals Whole-Genome Sequence of a Plant Growth-Promoting Strain, Serratia marcescens BTL07, Isolated from the Rhizoplane of Capsicum annuum L.

2020 ◽  
Vol 9 (18) ◽  
Author(s):  
Sudipta Dutta ◽  
Amena Khatun ◽  
Dipali Rani Gupta ◽  
Musrat Zahan Surovy ◽  
M. Mahbubur Rahman ◽  
...  
Keyword(s):  
Plant Growth ◽  
Serratia Marcescens ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Growth Promotion ◽  
Draft Genome ◽  
Plant Diseases ◽  
Whole Genome Sequence ◽  
Content Type

Serratia marcescens strain BTL07, which has the ability to promote growth and suppress plant diseases, was isolated from the rhizoplane of a chili plant. The draft genome sequence data of the strain will contribute to advancing our understanding of the molecular mechanisms underlying plant growth promotion and tolerance to different stresses.

scholarly journals Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1830
Author(s):  
Victor B. Pedrosa ◽  
Flavio S. Schenkel ◽  
Shi-Yi Chen ◽  
Hinayah R. Oliveira ◽  
Theresa M. Casey ◽  
...  
Keyword(s):  
Milk Production ◽  
Genome Sequence ◽  
North American ◽  
Milk Fat ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Holstein Cattle ◽  
Whole Genome ◽  
Production Traits

Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2742-2751 ◽  
Author(s):  
Henryk Urbanczyk ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Taxonomic Revision ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
The Family

Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.

scholarly journals Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

2019 ◽  
Author(s):  
Antonis Kioukis ◽  
Vassiliki A. Michalopoulou ◽  
Laura Briers ◽  
Stergios Pirintsos ◽  
David J. Studholme ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Sequence Data ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Crop Wild Relatives ◽  
Demographic Model ◽  
Sequencing Data

AbstractCrop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica.De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins.Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.

scholarly journals Draft genome sequence of the strain 16-537536, isolated from a patient with bronchiectasis and its relationship to the Pseudomonas koreensis group of the Pseudomonas fluorescens complex

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ad. C. Fluit ◽  
Malbert R. C. Rogers ◽  
María Díez-Aguilar ◽  
Rafael Cantón ◽  
Barry J. Benaissa-Trouw ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Antibiotic Resistance Gene ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Correct Identification ◽  
Whole Genome

Abstract Objective The Pseudomonas koreensis group bacteria are usually found in soil and are associated with plants. Currently they are poorly described. Here we report on the whole genome sequence of a bacterial isolate from a patient with bronchiectasis that was first identified as P. koreensis, and on its position in the P. koreensis group. Results Strain 16-537536 was isolated from a patient with bronchiectasis from Spain and initially identified by MALDI-TOF as P. koreensis, a member of the Pseudomonas fluorescens complex. However, the average nucleotide identity analysis (ANIb) and whole genome alignments of the draft genome sequence of this strain showed it to be a member of the P. koreensis group of the P. fluorescens complex, but belonging to an undescribed species. In addition, based on ANIb analysis, the P. koreensis group contains several other unnamed species. Several genes for putative virulence factors were identified. The only antibiotic resistance gene present in strain 16-537536 was a class C β-lactamase. The correct identification of bacterial species from patients is of utmost importance in order to understand their pathogenesis and to track the potential spread of pathogens between patients. Whole genome sequence data should be included for the description of new species.

scholarly journals Draft Genome Sequence of Ciprofloxacin and Ceftriaxone Resistant Campylobacter jejuni MM26-781 Assigned to Novel ST Isolated From Common Pigeon in Lithuania

2019 ◽  
Vol 15 ◽  
pp. 117693431986846
Author(s):  
Jurgita Aksomaitiene ◽  
Sigita Ramonaite ◽  
Aleksandr Novoslavskij ◽  
Mindaugas Malakauskas ◽  
Egle Kudirkiene
Keyword(s):  
Antibiotic Resistance ◽  
Campylobacter Jejuni ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Columba Livia ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wide Range

Campylobacter jejuni is an important zoonotic pathogen known to be resistant to a wide range of antibiotics worldwide. Campylobacter jejuni may be intrinsically resistant to antibiotics or can acquire antibiotic resistance determinants through gene transfer. However, the knowledge of molecular mechanisms of antimicrobial resistance among Campylobacter isolates from wild birds, especially in Lithuania, is limited. Whole genome sequencing (WGS) is a tool for better understanding the evolutionary and epidemiologic dynamics of C jejuni. This study describes a draft whole genome sequence of C jejuni MM26-781 isolated from a common pigeon ( Columba livia) in Lithuania in 2011 and assigned to ST-6424 (CC179) sequence type. The draft genome sequence contained 1.68 Mb, comprising 1651 coding genes, 40 transfer RNAs, 1 ribosomal RNA, and 69 pseudogenes with an average G + C content of 30.4%. The RAST (Rapid Annotation using Subsystem Technology) pipeline annotated (NCTC11168) a total of 305 subsystems in the genome of C jejuni MM26-781 strain, with most of the genes associated with amino acids and derivatives related to metabolism (18.93%) and protein metabolism (14.43%). The genes and mutations related to antibiotic resistance, including gyrA and gyrB genes associated with quinolone resistance, blaOXA-448 gene (locus tag C9371_07715) associated with resistance to β-lactams, rpoB gene associated with resistance to rifamycin, vgaE gene associated with resistance to streptogramin and efflux system CmeABC ( cmeA, cmeB, cmeC), efflux pump PmrA, and transcriptional regulator CmeR responsible for multidrug resistance in C jejuni MM26-781 chromosome, were identified. Also, the virulence factors, including ciaB, cadF, ceuE, pldA, motB, and bd1A genes, were identified by WGS data analysis.

scholarly journals Whole-Genome Sequence of Enterobacter sp. Strain MF024, Isolated from Soil in Shanghai, China

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Shaofeng Rong ◽  
Jin Wu ◽  
Qianqian Li ◽  
Shuo Zhang ◽  
Baoguo Cai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Ehrlich Pathway ◽  
Potential Use

We report here the draft genome sequence of Enterobacter sp. strain MF024, a bacterium that can biosynthesize 2-phenylethanol through both the Ehrlich pathway and a de novo pathway. It has potential use for the production of 2-phenylethanol.

scholarly journals Draft Genome Sequences of 28 Actinobacteria of the Family Microbacteriaceae Associated with Nematode-Infected Plants

2021 ◽  
Vol 10 (9) ◽  
Author(s):  
Sergey V. Tarlachkov ◽  
Irina P. Starodumova ◽  
Lubov V. Dorofeeva ◽  
Natalia V. Prisyazhnaya ◽  
Tatiana V. Roubtsova ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Draft Genome ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Genome Sequences ◽  
The Family ◽  
Baseline Information ◽  
Plant Parasitic

ABSTRACT Draft genome sequences of 28 strains of Microbacteriaceae from plants infested by plant-parasitic nematodes were obtained using Illumina technology. The sequence data will provide useful baseline information for the development of comparative genomics and systematics of Microbacteriaceae and facilitate understanding of molecular mechanisms involved in interactions between plants and nematode-associated bacterial complexes.

scholarly journals Whole-Genome Sequence of Monascus purpureus GB-01, an Industrial Strain for Food Colorant Production

2019 ◽  
Vol 8 (24) ◽  
Author(s):  
Toshitaka Kumagai ◽  
Masatoshi Tsukahara ◽  
Naoya Katayama ◽  
Katsuro Yaoi ◽  
Sachiyo Aburatani ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Monascus Purpureus ◽  
Whole Genome Sequence ◽  
Industrial Strain ◽  
Content Type ◽  
Sequencing Errors ◽  
Food Colorant ◽  
Long Reads

We report the draft genome sequence of Monascus purpureus GB-01, an industrial strain used as a food colorant. De novo assembly of long reads resulted in 121 chromosomal contigs and 1 mitochondrial contig, and sequencing errors were corrected by paired-end short reads. This genome sequence will provide useful information for azaphilone pigments and mycotoxin citrinin biosynthesis.

scholarly journals De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data

2017 ◽  
Vol 35 (3) ◽  
pp. 593-606 ◽  
Author(s):  
Helle Tessand Baalsrud ◽  
Ole Kristian Tørresen ◽  
Monica Hongrø Solbakken ◽  
Walter Salzburger ◽  
Reinhold Hanel ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gene Evolution ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Antifreeze Glycoproteins ◽  
Genome Sequence Data ◽  
De Novo Gene
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