scholarly journals Previously undetected superspreading of Mycobacterium tuberculosis revealed by deep sequencing

2019 ◽  
Author(s):  
Robyn S. Lee ◽  
Jean-François Proulx ◽  
Fiona McIntosh ◽  
Marcel A. Behr ◽  
William P. Hanage
Keyword(s):  
Deep Sequencing ◽  
Reference Genome ◽  
Transmission Dynamics ◽  
The Arctic ◽  
Smrt Sequencing ◽  
Host Diversity ◽  
Genomic Analyses ◽  
Local Reference ◽  
Genomic Studies ◽  
Pacbio Smrt Sequencing

AbstractTuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether ‘deep’ sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from the Arctic (2011-2012, 50 cases). Samples were sequenced to ~500-1000x and reads were aligned to a novel local reference genome generated with PacBio SMRT sequencing. Consensus and heterogeneous variants were identified and compared across genomes. In contrast with previous genomic analyses using ~50x depth, deep sequencing allowed us to identify a novel super-spreader who likely transmitted to up to 17 other cases during the outbreak (35% of all cases that year). It is increasingly evident that within-host diversity should be incorporated into transmission analyses; deep sequencing can facilitate accurately detection of super-spreaders and corresponding transmission clusters. This has implications not only for TB, but all genomic studies of transmission - regardless of pathogen.

scholarly journals Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Robyn S Lee ◽  
Jean-François Proulx ◽  
Fiona McIntosh ◽  
Marcel A Behr ◽  
William P Hanage
Keyword(s):  
Deep Sequencing ◽  
Reference Genome ◽  
Transmission Dynamics ◽  
The Arctic ◽  
Smrt Sequencing ◽  
Host Diversity ◽  
Genomic Analyses ◽  
Local Reference ◽  
Genomic Studies ◽  
Pacbio Smrt Sequencing

Tuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether ‘deep’ sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from the Arctic (2011–2012, 50 cases). Samples were sequenced to ~500–1000x and reads were aligned to a novel local reference genome generated with PacBio SMRT sequencing. Consensus and heterogeneous variants were identified and compared across genomes. In contrast with previous genomic analyses using ~50x depth, deep sequencing allowed us to identify a novel super-spreader who likely transmitted to up to 17 other cases during the outbreak (35% of the remaining cases that year). It is increasingly evident that within-host diversity should be incorporated into transmission analyses; deep sequencing may facilitate more accurate detection of super-spreaders and transmission clusters. This has implications not only for TB, but all genomic studies of transmission - regardless of pathogen.

Population-tailored mock genome enables genomic studies in species without a reference genome

2021 ◽  
Author(s):  
Felipe Sabadin ◽  
Humberto Fanelli Carvalho ◽  
Giovanni Galli ◽  
Roberto Fritsche-Neto
Keyword(s):  
Reference Genome ◽  
Genomic Studies

scholarly journals Complete Genome Sequence of Potential Probiotic Lactobacillus sp. HFC8, Isolated from Human Gut Using PacBio SMRT Sequencing

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Madhu Kumari ◽  
Mohit Kumar Swarnkar ◽  
Sanjay Kumar ◽  
Anil Kumar Singh ◽  
Mahesh Gupta
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacteriocin Production ◽  
Smrt Sequencing ◽  
Human Gut ◽  
Gene Coding ◽  
Probiotic Lactobacillus ◽  
Pacbio Smrt Sequencing ◽  
Production Cell

We report a 3.07-Mb complete genome sequence of a lactic acid bacterium, Lactobacillus sp. HFC8. The gene-coding clusters are predicated for probiotic characteristics, like bacteriocin production, cell adhesion, bile salt hydrolysis, lactose metabolism, autoaggregation, and tolerance to oxidative stress.

scholarly journals Comparative chloroplast genomic analyses revealed extensive genomic arrangement in some core and non-core caryophyllales

2019 ◽  
Vol 26 (1) ◽  
pp. 106-117 ◽  
Author(s):  
M. Ajmal Ali
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationship ◽  
Reference Genome ◽  
Gene Organization ◽  
Genomic Rearrangement ◽  
Coding Region ◽  
Genomic Arrangement ◽  
Genomic Analyses

The order Caryophyllales exhibit diverse diversity in morphology to molecules, which leads to taxonomic complexities in circumscribing especially to its families. The comparative analysis of the available chloroplast genome to detect pattern of genomic arrangement and variation is lacking; hence, the alignment pattern and genomic rearrangement across the Caryophyllales were detected, and the phylogenetic relationship among the families of the Caryophyllales based on maximum cp genes were inferred. The comparison of the Caryophyllales cp genomes based on representatives of 10 families with Taxillus chinensis as reference genome revealed that coding region were more conserved than the non-coding region; however, clpP, rpl16 and ycf15 were the most divergent coding region among all taxa. Further, the genomic rearrangement occurred in gene organization of the taxa among different families of Caryophyllales, the extensive rearrangement were observed in Amaranthaceae, Caryophyllaceae, Chenopodiaceae,Droseraceae and Cactaceae.

scholarly journals The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisong Hu ◽  
Zhongping Xu ◽  
Maojun Wang ◽  
Rui Fan ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Families ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Phylogenomic Analysis ◽  
Genomic Analyses ◽  
Species Specific ◽  
Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

scholarly journals Genome Report: A highly contiguous reference genome for Northern Bobwhite (Colinus virginianus)

2019 ◽  
Author(s):  
Jessie F. Salter ◽  
Oscar Johnson ◽  
Norman J. Stafford ◽  
William F. Herrin ◽  
Darren Schilling ◽  
...  
Keyword(s):  
Reference Genome ◽  
Colinus Virginianus ◽  
Phenotypic Diversity ◽  
Northern Bobwhite ◽  
Wild Female ◽  
Tissue Samples ◽  
Future Studies ◽  
Northern Bobwhites ◽  
Assembly Pipeline ◽  
Genomic Studies

ABSTRACTNorthern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. Using Dovetail Chicago and HiC libraries with the HiRise assembly pipeline, we produced an 866.8 Mbp assembly including 1,512 scaffolds with a contig N50 of 66.8 Mbp, a scaffold L50 of four, and a BUSCO completeness score of 90.8%. This new assembly greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.

scholarly journals Fully resolved assembly of Cryptosporidium parvum

2021 ◽  
Author(s):  
Vipin K. Menon ◽  
Pablo C. Okhuysen ◽  
Cynthia Chappell ◽  
Medhat Mahmoud ◽  
Qingchang Meng ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Reference Genome ◽  
Single Copy ◽  
Comparative Genomic ◽  
Infection Prevalence ◽  
High Quality ◽  
Apicomplexan Parasites ◽  
Oxford Nanopore ◽  
Genomic Study ◽  
Genomic Studies

Background Cryptosporidium parvum are apicomplexan parasites commonly found across many species with a global infection prevalence of 7.6%. As such it is important to understand the diversity and genomic makeup of this prevalent parasite to prohibit further spread and to fight an infection. The general basis of every genomic study is a high quality reference genome that has continuity and completeness, and is of high quality and thus enables comprehensive comparative studies. Findings Here we provide a highly accurate and complete reference genome of Cryptosporidium spp.. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall the assembly shows a high completion rate with 98.4% single copy Busco genes. This is also shown by the identification of 13 telomeric regions across the 8 chromosomes. The consensus accuracy of the established reference genome was further validated by sequence alignment of established genetic markers for C.parvum. Conclusions This high quality reference genome provides the basis for subsequent studies and comparative genomic studies across the Cryptosporidium clade.

scholarly journals SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis

2016 ◽  
Author(s):  
Afif Elghraoui ◽  
Samuel J Modlin ◽  
Faramarz Valafar
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Molecule ◽  
Genetic Basis ◽  
Reference Genome ◽  
Reference Sequence ◽  
Smrt Sequencing ◽  
Virulence Attenuation ◽  
Sequencing Platforms ◽  
Genome Comparisons ◽  
Reference Genomes

AbstractThe genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of its virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. We discuss how our results change the picture of virulence attenuation and the power of SMRT sequencing for producing high-quality reference genomes.

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