scholarly journals The complete genome sequences of Erythroxylum coca and Erythroxylum novogranatense

2022 ◽  
Author(s):  
Dawson White ◽  
Lyndel Meinhardt ◽  
Bryan Bailey ◽  
Stacy Pirro
Keyword(s):  
South America ◽  
Complete Genome ◽  
De Novo ◽  
Flowering Plant ◽  
Genome Sequences ◽  
The Andes

Abstract The flowering plant genus Erythroxylum contains approximately 300 species, including the economically and socially consequential crops called coca. We present the genome sequences of Erythroxylum coca and E. novogranatense, two cultigens produced for medicinal and quotidian use in the Andes and Amazon regions of South America, as well as the international cocaine industry. Sequencing was performed on an Illumina X-Ten platform, and reads were assembled by a de novo method followed by finishing via comparison with several species from the same genus. The BioProject, raw and assembled data can be accessed in GenBank for E. coca (PRJNA676123; JAJMLV000000000) and E. novogranatense (PRJNA675212; JAJKBF000000000)

scholarly journals Genome Resource of Two Potato Strains of Ralstonia solanacearum Biovar 2 (Phylotype IIB Sequevar 1) and Biovar 2T (Phylotype IIB Sequevar 25) Isolated from Lowlands in Iran

2020 ◽  
Vol 33 (7) ◽  
pp. 872-875 ◽  
Author(s):  
Nasim Sedighian ◽  
Marjon Krijger ◽  
Tanvi Taparia ◽  
S. Mohsen Taghavi ◽  
Emmanuel Wicker ◽  
...  
Keyword(s):  
South America ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Complete Genome ◽  
Genomic Data ◽  
Brown Rot ◽  
Genome Sequences ◽  
Rot Disease ◽  
Tropical Lowlands ◽  
Major Pathogens

Ralstonia solanacearum, the causal agent of bacterial wilt and brown rot disease, is one of the major pathogens of solanaceous crops, including potato, around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and is only reported in South America and Iran. Thus far, no genome resource of the biovar 2T of the pathogen has been available. Here, we present the near-complete genome sequences of the biovar 2T strain CFBP 8697 as well as strain CFBP 8695 belonging to biovar 2 race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum and pave the way for research on biovar 2T functional and interaction genetics.

scholarly journals First complete genome sequences of Streptococcus pyogenes NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies

2020 ◽  
Author(s):  
Francisco Salvà-Serra ◽  
Daniel Jaén-Luchoro ◽  
Hedvig E. Jakobsson ◽  
Lucia Gonzales-Siles ◽  
Roger Karlsson ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Streptococcus Pyogenes ◽  
Complete Genome ◽  
Type Strain ◽  
Type Species ◽  
De Novo ◽  
Genome Sequences ◽  
Sequence Identity ◽  
Oxford Nanopore ◽  
Infectious Disease Diagnostics

AbstractWe present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies, yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes.These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.

scholarly journals Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Antonio D. Moreno ◽  
Christian Tellgren-Roth ◽  
Lucile Soler ◽  
Jacques Dainat ◽  
Lisbeth Olsson ◽  
...  
Keyword(s):  
Complete Genome ◽  
De Novo ◽  
Biofuel Production ◽  
Lignocellulosic Materials ◽  
Genome Sequences ◽  
Content Type ◽  
Candida Intermedia ◽  
Genome Assemblies

ABSTRACT Sustainable biofuel production from lignocellulosic materials requires efficient and complete use of all abundant sugars in the biomass, including xylose. Here, we report on the de novo genome assemblies of two strains of the xylose-fermenting yeast Candida intermedia: CBS 141442 and PYCC 4715.

scholarly journals Complete Genome Sequences of Peach Latent Mosaic Viroid from a Single Peach Cultivar

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Yeonhwa Jo ◽  
Su-Hyun Yoo ◽  
Hyosub Chu ◽  
Jin Kyong Cho ◽  
Hoseong Choi ◽  
...  
Keyword(s):  
Complete Genome ◽  
Sanger Sequencing ◽  
De Novo ◽  
Genome Sequences ◽  
Peach Cultivar ◽  
The Family ◽  
Peach Trees

Peach latent mosaic viroid (PLMVd) is a member of the genus Pelamoviroid in the family Avsunviroidae and infects peach trees. We de novo assembled a PLMVd genome from a peach transcriptome and identified 18 variants in a single peach cultivar, after sequencing 20 PLMVd genomes by Sanger sequencing.

scholarly journals Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia

2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Piroon Jenjaroenpun ◽  
Thidathip Wongsurawat ◽  
Zulema Udaondo ◽  
Courtney Anderson ◽  
James Lopez ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Complete Genome ◽  
De Novo ◽  
Sequence Data ◽  
Resistance Mutations ◽  
Genome Sequences ◽  
Content Type ◽  
Vana Gene ◽  
Illumina Sequence ◽  
Vancomycin Resistant

Here, we present complete genome sequences of four Enterococcus faecium isolates, obtained from two patients with apparent vancomycin-resistant Enterococcus faecium bacteremia; these isolates also carried two mutations known to be associated with daptomycin resistance. Sequences were obtained using de novo and hybrid assembly of Oxford Nanopore and Illumina sequence data.

scholarly journals On the (Im)possibility to Reconstruct Plasmids from Whole Genome Short-Read Sequencing Data

2016 ◽  
Author(s):  
Sergio Arredondo-Alonso ◽  
Willem van Schaik ◽  
Rob J. Willems ◽  
Anita C. Schürch
Keyword(s):  
Complete Genome ◽  
De Novo ◽  
Bacterial Genome ◽  
Composition Analysis ◽  
Bacterial Survival ◽  
Sequencing Data ◽  
Genome Sequences ◽  
High Throughput Analysis ◽  
Short Read ◽  
Short Read Sequencing

AbstractPlasmids are autonomous extra-chromosomal elements in bacterial cells that can carry genes that are important for bacterial survival. To benchmark algorithms for automated plasmid sequence reconstruction from short read sequencing data, we selected 42 publicly available complete bacterial genome sequences which were assembled by a combination of long- and short-read data. The selected bacterial genome sequence projects span 12 genera, containing 148 plasmids. We predicted plasmids from short-read data with four different programs (PlasmidSPAdes, Recycler, cBar and PlasmidFinder) and compared the outcome to the reference sequences.PlasmidSPAdes reconstructs plasmids based on coverage differences in the assembly graph. It reconstructed most of the reference plasmids (recall = 0.82) but approximately a quarter of the predicted plasmid contigs were false positives (precision = 0.76). PlasmidSPAdes merged 83 % of the predictions from genomes with multiple plasmids in a single bin. Recycler searches the assembly graph for sub-graphs corresponding to circular sequences and correctly predicted small plasmids but failed with long plasmids (recall = 0.12, precision = 0.30). cBar, which applies pentamer frequency composition analysis to detect plasmid-derived contigs, showed an overall recall and precision of 0.78 and 0.64. However, cBar only categorizes contigs as plasmid-derived and does not bin the different plasmids correctly within a bacterial isolate. PlasmidFinder, which searches for matches in a replicon database, had the highest precision (1.0) but was restricted by the contents of its database and the contig length obtained from de novo assembly (recall = 0.36).Surprisingly, PlasmidSPAdes and Recycler detected single isolated components corresponding to putative novel small plasmids (<10 kbp) which were also predicted as plasmids by cBar.This study shows that it is possible to automatically predict plasmid sequences, but only for small plasmids. The reconstruction of large plasmids (>50 kbp) containing repeated sequences remains challenging and limits the high-throughput analysis of WGS data.Author SummaryShort read sequencing of the DNA of bacteria is often used to understand characteristics such as antibiotic resistance. However the assembly of short read sequencing data with the goal of reconstructing a complete genome is often fragmented and leaves gaps. Therefore independently replicating DNA fragments called plasmids cannot easily be identified from an assembly. Lately a number of programs have been developed to enable the automated prediction of the sequences of plasmids. Here we tested these programs by comparing their outcomes with complete genome sequences. None of the tested programs were able to fully and unambiguously predict distinct plasmid sequences. All programs performed best with the prediction of plasmids smaller than 50 kbp. Larger plasmids were only correctly predicted if they were present as a single contig in the assembly. While predictions by PlasmidSPAdes and cBar contained most of the plasmids, they were merged with or indistinguishable from other plasmids and sometimes chromosome sequences. PlasmidFinder missed most plasmids but all its predictions were correct. Without manual steps or long-read sequencing information, plasmid reconstruction from short read sequencing data remains challenging.

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

scholarly journals Future climate change will impact the size and location of breeding and wintering areas of migratory thrushes in South America

The Condor ◽  
2021 ◽  
Author(s):  
Natália Stefanini Da Silveira ◽  
Maurício Humberto Vancine ◽  
Alex E Jahn ◽  
Marco Aurélio Pizo ◽  
Thadeu Sobral-Souza
Keyword(s):  
Climate Change ◽  
South America ◽  
Migratory Birds ◽  
Global Climate ◽  
Future Climate ◽  
Future Climate Change ◽  
Ecological Niche Models ◽  
Global Climate Changes ◽  
The Andes ◽  
Wintering Areas

Abstract Bird migration patterns are changing worldwide due to current global climate changes. Addressing the effects of such changes on the migration of birds in South America is particularly challenging because the details about how birds migrate within the Neotropics are generally not well understood. Here, we aim to infer the potential effects of future climate change on breeding and wintering areas of birds that migrate within South America by estimating the size and elevations of their future breeding and wintering areas. We used occurrence data from species distribution databases (VertNet and GBIF), published studies, and eBird for 3 thrush species (Turdidae; Turdus nigriceps, T. subalaris, and T. flavipes) that breed and winter in different regions of South America and built ecological niche models using ensemble forecasting approaches to infer current and future potential distributions throughout the breeding and wintering periods of each species. Our findings point to future shifts in wintering and breeding areas, mainly through elevational and longitudinal changes. Future breeding areas for T. nigriceps, which migrates along the Andes Mountains, will be displaced to the west, while breeding displacements to the east are expected for the other 2 species. An overall loss in the size of future wintering areas was also supported for 2 of the species, especially for T. subalaris, but an increase is anticipated for T. flavipes. Our results suggest that future climate change in South America will require that species shift their breeding and wintering areas to higher elevations in addition to changes in their latitudes and longitude. Our findings are the first to show how future climate change may affect migratory birds in South America throughout the year and suggest that even closely related migratory birds in South America will be affected in different ways, depending on the regions where they breed and overwinter.

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