The whole-genome data is publicly available in the Nucleotide Sequence Archive (CNSA) of China National GeneBank (CNGB) (https://db.cngb.org/cnsa/) ... Liang, HongpingWang, HongliXu, YanLi LinzhouMelkonian, BarbaraLorenz, MaikeFriedl, ThomasSahu, Sunil KumarYu, JinLiu, HuanMelkonian, Michae...
oxysporum based on morphological characteristics, PCR amplification [11], a phylogenetic analysis based on the nucleotide sequences of cmdA, rpb2, tef1, and tub2, and a pathogenicity test with 1-year-old healthy seedlings of K. roxburghii, which fulfilled Koch′s postulates [4]. Strain By...
These members come from a wide range of biomedical databases including those from 3 member databases of International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org): GenBank (http://www.ncbi.nlm.nih.gov/genbank), European Nucleotide Archive (ENA; http://www.ebi.ac....
All sequencing data were subjected to a series of quality control before further analysis with criteria: (1) base quality (Q30) > 80%; (2) mean sequence depth > 30×; (3) mapping rate ≥ 95%; (4) mismatch rate < 1%; (5) duplicate rate < 10%; (6) 20× ...
Phylogenetic analyses were then performed using the nucleotide sequences of various CoV gene datasets: (1) whole genome, (2) ORF1a, (3) ORF1b, (4) nsp5 (3CLpro), (5) RdRp (nsp12), (6) nsp13 (Hel), (7) nsp14 (ExoN), (8) nsp15 (NendoU), (9) nsp16 (O-MT), (10) ...
F. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 4, 41, https://doi.org/10.1186/1741-7007-4-41 (2006). Article CAS PubMed PubMed Central Google Scholar Keilwagen, J. et al. Using intron position conservation for homology...
Over 19 million single nucleotide polymorphisms (SNPs) and 1.98 million insertion-deletions (InDels) were identified using the reference genome (GRCg7b), further contributing to the public database. This dataset provides valuable resources for studying genetic diversity and adaptation and for the ...
In the first round, 200 bootstrap replicates were run, and GTRGAMMA was used as the nucleotide substitution model. On the basis of the phylogenetic topologies obtained and their bootstrap values, we selected a few representative reference sequences and formed eight smaller data sets. Phylogenetic ...
Sequencing reads have been submitted to the European Nucleotide Archive (EMBL-EBI) under study accession PRJEB23157. The geographic information for individual isolates is listed in Supplementary Table 3. The analysis scripts used in this study are available online at GitHub (https://github.com/Stop...
The raw Illumina, Oxford Nanopore, and Hi-C sequencing data are deposited on the NCBI Sequence Read Archive database under the accession numbers: SRR28581579, SRR28579687, and SRR28579680, respectively69. The genome assembly has been deposited on the NCBI GenBank database under the accession numb...