scholarly journals Genome sequence of Dichelobacter nodosus JKS-07B isolate from J&K, India associated with virulent footrot of sheep

2021 ◽  
Vol 104 (4) ◽  
pp. 003685042110576
Author(s):  
Sabia Qureshi ◽  
Shakil A Wani ◽  
Shaheen Farooq ◽  
Zahid Kashoo ◽  
Basharat Bhat ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Gc Content ◽  
Economic Losses ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Growth And Survival ◽  
Dichelobacter Nodosus ◽  
New Genes ◽  
Potential Vaccine ◽  
Efficacious Vaccine

Introduction: Virulent footrot of sheep caused by Dichelobacter nodosus is associated with tremendous economic losses due to recurrent treatment costs and increased culling rates. This organism being a fastidious anaerobe is difficult to isolate on ordinary media that does not support its growth. The D. nodosus serogroup B isolate described in the present study has been used in the preparation of the whole-cell killed vaccine against footrot in India. D. nodosus serogroup B is the predominant serogroup involved in virulent footrot (lesion score 4) in India as well as in many sheep-rearing countries of the globe. Methods: Genomic DNA was extracted using wizard Genomic DNA purification kit. The whole genome of the D. nodosus strain B was sequenced using an Illumina HiSeq 2500 platform and annotated according to functional gene categories. Annotations were performed using in-house developed Perl scripts using Nr/Nt database, uniprot, Pfam, KEGG, Panther DB, and GO database. Result: The assembled genome size is 1.311,533 Mb and GC content is 44.38. A total of 1215 protein-coding genes, 44tRNA and 7 rRNA were identified. The genome shows 98.63% sequence homology with the reference genome. However, 21 new genes have been identified in this genome. The information will provide insights into the various genes and regulators necessary for D. nodosus growth and survival. Discussion: The genome information of this serogroup B of D. nodosus isolate involved in 85–90% cases of virulent footrot of sheep in India provides further insights for improvement of the killed vaccine (B serogroup) developed recently in India. For the development of an efficacious vaccine against virulent footrot, it is essential to know the serological diversity as well as the virulent status of the strains of the D. nodosus. This serogroup isolate is a potential vaccine candidate to mitigate ovine footrot in India as the majority of virulent footrot cases belong to serogroup B of D. nodosus.

The mitochondrial genome and phylogenetic analysis of the tick Dermacentor everestianus Hirst, 1926 (Acari: Ixodidae)

2018 ◽  
Vol 23 (7) ◽  
pp. 1313 ◽  
Author(s):  
Zhijun Yu ◽  
Shiqi Zhang ◽  
Tianhong Wang ◽  
Xiaolong Yang ◽  
Hui Wang ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Gc Content ◽  
Ixodid Tick ◽  
Tibet Plateau ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Illumina Hiseq Sequencing ◽  
Dermacentor Everestianus ◽  
Mt Genome ◽  
Rna Genes

The tick Dermacentor everestianus is widely distributed in Qinghai-Tibet Plateau of China and can transmit many zoonotic pathogens. In the current study, the complete mitochondrial (mt) genome of D. everestianus was sequenced through Illumina HiSeq sequencing. The mt genome is 15,191 bp in length which contains 37 genes, including 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. The overall GC content reached 21.20%, whereas the GC content in the gene region was 21.40%, and in the intergenetic region was 20.50%. Two control regions were sequenced from mt genome of D. everestianus, one located between tRNA-Cys and tRNA-Leu, and the other one was found between rrnS and tRNA-Ile. Two tandem repeats were found between tRNA-Glu and nad1. A phylogenetic tree was constructed based on the complete mitogenome of D. everestianus and 32 other ixodid tick mitogenomes to assess their phylogenetic relationships. D. everestianus is phylogenetically clustered with the tick D. silvarum and D. nuttalli. This is the first complete mt genome of D. everestianus, which provides a useful reference for future studies on systematics and population genetics of this tick species.

scholarly journals The whole-genome sequence analysis of Morchella sextelata

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mei-Han ◽  
Qingshan-Wang ◽  
Baiyintala ◽  
Wuhanqimuge
Keyword(s):  
De Novo ◽  
Gc Content ◽  
Gene Clusters ◽  
Essential Amino Acids ◽  
Biologically Active ◽  
Whole Genome Sequence ◽  
Daily Consumption ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Morphological Studies

Abstract Morchella are macrofungi and are also called morels, as they exhibit a morel-like upper cap structure. Morels contain abundant essential amino acids, vitamins and biologically active compounds, which provide substantial health benefits. Approximately 80 species of Morchella have been reported, and even more species have been isolated. However, the lack of wild Morchella resources and the difficulties associated with culturing Morchella have caused a shortage in the morels available for daily consumption. Additionally, in-depth genomic and morphological studies are still needed. In this study, to provide genomic data for further investigations of culturing techniques and the biological functions of Morchella sextelata (M. sextelata), de novo genome sequencing was carried out on the Illumina HiSeq. 4000 platform using both the Illumina 150 and PacBio systems. The final estimated genome size of M. sextelata was 52.93 Mb, containing 59 contigs and a GC content of 47.37%. A total of 9,550 protein-coding genes were annotated. In addition, the repeat sequences, gene components and gene functions were analyzed using various databases. Furthermore, the secondary metabolite gene clusters and the predicted structures of their products were analyzed. Finally, a genomic comparison of different species of Morchella was performed.

scholarly journals Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig

2020 ◽  
Vol 9 (34) ◽  
Author(s):  
Binghui Zhou ◽  
Leonardo Albarracin ◽  
Yuki Masumizu ◽  
Yuhki Indo ◽  
M. Aminul Islam ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Intestinal Tract ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
A Genome

ABSTRACT Ligilactobacillus salivarius FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180 bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome.

scholarly journals Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 652
Author(s):  
Hongwei Tan ◽  
Muhammad Naeem ◽  
Hussain Ali ◽  
Muhammad Shakeel ◽  
Haiou Kuang ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Genome Sequence ◽  
Apis Cerana ◽  
Gc Content ◽  
Protein Domain ◽  
Pollination Services ◽  
Protein Coding ◽  
Close Relationship ◽  
Genome Scale ◽  
Asian Honeybee

In Pakistan, Apis cerana, the Asian honeybee, has been used for honey production and pollination services. However, its genomic makeup and phylogenetic relationship with those in other countries are still unknown. We collected A. cerana samples from the main cerana-keeping region in Pakistan and performed whole genome sequencing. A total of 28 Gb of Illumina shotgun reads were generated, which were used to assemble the genome. The obtained genome assembly had a total length of 214 Mb, with a GC content of 32.77%. The assembly had a scaffold N50 of 2.85 Mb and a BUSCO completeness score of 99%, suggesting a remarkably complete genome sequence for A. cerana in Pakistan. A MAKER pipeline was employed to annotate the genome sequence, and a total of 11,864 protein-coding genes were identified. Of them, 6750 genes were assigned at least one GO term, and 8813 genes were annotated with at least one protein domain. Genome-scale phylogeny analysis indicated an unexpectedly close relationship between A. cerana in Pakistan and those in China, suggesting a potential human introduction of the species between the two countries. Our results will facilitate the genetic improvement and conservation of A. cerana in Pakistan.

scholarly journals Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1169
Author(s):  
Xin Li ◽  
Xiaocen Wang ◽  
Pengtao Gong ◽  
Nan Zhang ◽  
Xichen Zhang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Genetic Manipulation ◽  
Molecular Genetic ◽  
Gc Content ◽  
Giardia Duodenalis ◽  
Codon Usage Pattern ◽  
Protein Size ◽  
New Genes ◽  
Optimal Codons ◽  
Usage Patterns

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

scholarly journals Gene prediction by multiple syntenic alignment

2005 ◽  
Vol 2 (1) ◽  
pp. 38-47
Author(s):  
Said S. Adi ◽  
Carlos E. Ferreira
Keyword(s):  
Computer Program ◽  
Genomic Dna ◽  
Gene Prediction ◽  
Genomic Sequences ◽  
Prediction Problem ◽  
Huge Amount ◽  
Protein Coding ◽  
Coding Regions ◽  
Conserved Regions ◽  
Similarity Information

Summary Given the increasing number of available genomic sequences, one now faces the task of identifying their functional parts, like the protein coding regions. The gene prediction problem can be addressed in several ways. One of the most promising methods makes use of similarity information between the genomic DNA and previously annotated sequences (proteins, cDNAs and ESTs). Recently, given the huge amount of newly sequenced genomes, new similarity-based methods are being successfully applied in the task of gene prediction. The so-called comparative-based methods lie in the similarities shared by regions of two evolutionary related genomic sequences. Despite the number of different gene prediction approaches in the literature, this problem remains challenging. In this paper we present a new comparative-based approach to the gene prediction problem. It is based on a syntenic alignment of three or more genomic sequences. With syntenic alignment we mean an alignment that is constructed taking into account the fact that the involved sequences include conserved regions intervened by unconserved ones. We have implemented the proposed algorithm in a computer program and confirm the validity of the approach on a benchmark including triples of human, mouse and rat genomic sequences.

scholarly journals Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Momchilo Vuyisich ◽  
Ayesha Arefin ◽  
Karen Davenport ◽  
Shihai Feng ◽  
Cheryl Gleasner ◽  
...  
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Gc Content ◽  
Library Preparation ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Dna Amount ◽  
High Quality ◽  
Preparation Methods

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing andde novoassembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing andde novoassembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderiaspp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing andde novoassembly is not decreased when only 10 ng of input genomic DNA is used.

scholarly journals Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Sarah Mederos da Silveira ◽  
Sheila da Silva ◽  
Andrew Macrae ◽  
Rommel T. J. Ramos ◽  
Fabrício A. Araújo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
South Shetland Islands ◽  
Deschampsia Antarctica ◽  
King George Island ◽  
Protein Coding ◽  
Content Type ◽  
Shetland Islands ◽  
Rhizosphere Bacterium

Pseudomonas sp. strain LAP_36 was isolated from rhizosphere soil from Deschampsia antarctica on King George Island, South Shetland Islands, Antarctica. Here, we report on its draft genome sequence, which consists of 8,794,771 bp with 60.0% GC content and 8,011 protein-coding genes.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

scholarly journals Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

2017 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Bernadette Renckens ◽  
Sacha A.F.T. van Hijum ◽  
Vitor A.P. Martins dos Santos ◽  
...  
Keyword(s):  
Amino Acids ◽  
Small Intestine ◽  
Short Chain Fatty Acids ◽  
Limited Capacity ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Mate Pair ◽  
Simple Carbohydrates

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC. Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.

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