scholarly journals Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Alessandra Traini ◽  
Massimo Iorizzo ◽  
Harpartap Mann ◽  
James M. Bradeen ◽  
Domenico Carputo ◽  
...  
Keyword(s):  
Genome Organization ◽  
Regulatory Networks ◽  
Reference Genome ◽  
Sequence Variability ◽  
Genome Sequences ◽  
Cultivated Potato ◽  
Diversity Arrays Technology ◽  
Genomic Tools ◽  
Structural Divergence ◽  
Microscale Heterogeneity

Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potatoSolanum tuberosum. Among them,S. bulbocastanumandS. commersoniiare well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes ofS. bulbocastanumand/orS. commersoniigenotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

scholarly journals Sequence variability ofChrysanthemum stunt viroidin different chrysanthemum cultivars

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2933 ◽  
Author(s):  
Hoseong Choi ◽  
Yeonhwa Jo ◽  
Ju-Yeon Yoon ◽  
Seung-Kook Choi ◽  
Won Kyong Cho
Keyword(s):  
Infectious Agents ◽  
Sequence Variability ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Genomic Variations ◽  
The Family ◽  
Chrysanthemum Plant ◽  
Single Nucleotide Variations ◽  
Polymerase Chain

Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein.Chrysanthemum stunt viroid(CSVd), a member of the familyPospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.

scholarly journals benchNGS : An approach to benchmark short reads alignment tools

2015 ◽  
Author(s):  
Farzana Rahman ◽  
Mehedi Hassan ◽  
Alona Kryshchenko ◽  
Inna Dubchak ◽  
Tatiana V Tatarinova ◽  
...  
Keyword(s):  
Reference Genome ◽  
Global Alignment ◽  
Short Report ◽  
Related Genome ◽  
Genome Sequences ◽  
Short Reads ◽  
Relevant Reference ◽  
Next Generation Sequencing Ngs ◽  
Reference Genomes ◽  
Generation Sequencing

In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance. We propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools .

scholarly journals De novo assembly of the cattle reference genome with single-molecule sequencing

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Benjamin D Rosen ◽  
Derek M Bickhart ◽  
Robert D Schnabel ◽  
Sergey Koren ◽  
Christine G Elsik ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Future Research ◽  
Protein Coding ◽  
Single Molecule Sequencing ◽  
Assembly Accuracy ◽  
Genomic Tools

Abstract Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

scholarly journals Comparative Genomics ofCryptosporidium

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Aurélien J. Mazurie ◽  
João M. Alves ◽  
Luiz S. Ozaki ◽  
Shiguo Zhou ◽  
David C. Schwartz ◽  
...  
Keyword(s):  
Genome Organization ◽  
Distinct Species ◽  
Genome Sequences ◽  
Cryptosporidium Hominis ◽  
Gene Deletions ◽  
Structural Alterations ◽  
Phenotypic Differences ◽  
Apicomplexan Parasites ◽  
Sequence Identity ◽  
Local Sequence

Until recently, the apicomplexan parasites,Cryptosporidium hominisandC. parvum, were considered the same species. However, the two parasites, now considered distinct species, exhibit significant differences in host range, infectivity, and pathogenicity, and their sequenced genomes exhibit only 95–97% identity. The availability of the complete genome sequences of these organisms provides the potential to identify the genetic variations that are responsible for the phenotypic differences between the two parasites. We compared the genome organization and structure, gene composition, the metabolic and other pathways, and the local sequence identity between the genes of these twoCryptosporidiumspecies. Our observations show that the phenotypic differences betweenC. hominisandC. parvumare not due to gross genome rearrangements, structural alterations, gene deletions or insertions, metabolic capabilities, or other obvious genomic alterations. Rather, the results indicate that these genomes exhibit a remarkable structural and compositional conservation and suggest that the phenotypic differences observed are due to subtle variations in the sequences of proteins that act at the interface between the parasite and its host.

scholarly journals Streptococcal taxonomy based on genome sequence analyses

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 67 ◽  
Author(s):  
Cristiane C Thompson ◽  
Vanessa E Emmel ◽  
Erica L Fonseca ◽  
Michel A Marin ◽  
Ana Carolina P Vicente
Keyword(s):  
Amino Acid Identity ◽  
Species Level ◽  
Viridans Streptococci ◽  
Genome Sequences ◽  
Sequence Analyses ◽  
Acid Identity ◽  
Genomic Signatures ◽  
Genomic Tools ◽  
Average Amino Acid Identity ◽  
Genomic Analyses

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance,S. pneumoniae,S. mitis, andS. oralis. AStreptococcusspecies can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

scholarly journals The Taxus genome provides insights into paclitaxel biosynthesis

2021 ◽  
Author(s):  
Xingyao Xiong ◽  
Junbo Gou ◽  
Qinggang Liao ◽  
Yanlin Li ◽  
Qian Zhou ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genome Duplication ◽  
Taxus Chinensis ◽  
Biosynthesis Pathway ◽  
Gene Duplications ◽  
Genome Sequences ◽  
Biotechnological Potential ◽  
Functional Grouping ◽  
Transposon Evolution ◽  
Chromosome Level

AbstractThe ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 Gb. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster in the taxadiene biosynthesis, which was mainly formed by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.One Sentence SummaryA chromosome-level genome assembly of Taxus chinensis var. mairei uncovers its unique genome evolution process and genetic architectures for the paclitaxel biosynthesis pathway.

scholarly journals Generation of small interfering RNA (siRNA) database from SARS-CoV-2 genome sequences

2020 ◽  
Author(s):  
Inácio Gomes Medeiros ◽  
André Salim Khayat ◽  
Beatriz Stransky ◽  
Sidney Emanuel Batista dos Santos ◽  
Paulo Pimentel de Assumpção ◽  
...  
Keyword(s):  
Human Genome ◽  
Design Process ◽  
Small Interfering Rna ◽  
Reference Genome ◽  
Second Phase ◽  
Computational Power ◽  
Genome Sequences ◽  
Interfering Rna ◽  
Reference Genomes

Abstract This protocol aims to describe the building of a database of SARS-CoV-2 targets for siRNA approaches. Starting from the virus reference genome, we will derive sequences from 18 to 21nt-long and verify their similarity against the human genome and coding and non-coding transcriptome, as well as genomes from related viruses. We will also calculate a set of thermodynamic features for those sequences and will infer their efficiencies using three different predictors. The protocol has two main phases: at first, we align sequences against reference genomes. In the second one, we extract the features. The first phase varies in terms of duration, depending on computational power from the running machine and the number of reference genomes. Despite that, the second phase lasts about thirty minutes of execution, also depending on the number of cores of running machine. The constructed database aims to speed the design process by providing a broad set of possible SARS-CoV-2 sequences targets and siRNA sequences.

scholarly journals New Reference Genome Sequences for 17 Bacterial Strains of the Honey Bee Gut Microbiota

2018 ◽  
Vol 7 (3) ◽  
Author(s):  
Kirsten M. Ellegaard ◽  
Philipp Engel
Keyword(s):  
Gut Microbiota ◽  
Honey Bee ◽  
Honey Bees ◽  
Reference Genome ◽  
Reference Database ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Content Type ◽  
Future Analysis ◽  
Comprehensive Reference

We sequenced the genomes of 17 strains isolated from the gut of honey bees, including strains representing the genera Lactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, Frischella, and Commensalibacter. These genome sequences represent an important step forward in the development of a comprehensive reference database to aid future analysis of this emerging gut microbiota model.

scholarly journals A Reference Genome Sequence for Giant Sequoia

2020 ◽  
Vol 10 (11) ◽  
pp. 3907-3919
Author(s):  
Alison D. Scott ◽  
Aleksey V. Zimin ◽  
Daniela Puiu ◽  
Rachael Workman ◽  
Monica Britton ◽  
...  
Keyword(s):  
Sierra Nevada ◽  
Genome Sequence ◽  
Reference Genome ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Reference Genome Sequence ◽  
Oxford Nanopore ◽  
Sierra Nevada Mountains ◽  
Genomic Tools ◽  
Giant Sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, were used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

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