General properties of genome draft for Burkholderia stabilis strain CH16 from Switzerland * Property Value Draft genome size, bp 8,505,958 Chromosomes 3 Chromosome sizes, bp 3,705,321; 3,499,410; 1,230,432 Plasmid size, bp 70,922 % G+C content 66.3 Predicted CDSs (per 7,629 (3,402; 3,068; 1,075; 84) chromosome and plasmid) Coding density 86.40% Average gene length 965 bp Pseudogenes
20 rRNA operons 6 tRNAs 75 Insertion elements 40 * CDSs, coding sequences.
When they analyzed the 2,764 genes that were present in only one or two of these reference annotations, they were surprised to discover that experimental evidence and manual annotations suggested that almost all of these genes were more likely to be non-coding genes or pseudogenes
. In fact, these genes, together with another 1,470 coding genes that are present in the three reference catalogs, were not evolving like typical protein coding genes.
This is the first application of a clinical NGS algorithm for copy number detection in a pseudogene
. Although not highly specific, this method has very high analytical sensitivity (10, this study) and is cost-effective because it only requires running a bioinformatics script on readily generated sequencing data.
was found for DPPA2 coding sequence which is important in primer design.
Pandolfi, "A coding-independent function of gene and pseudogene
mRNAs regulates tumour biology," Nature, vol.
Other subtype B genes that have become pseudogenes
in subtype A specimens and are associated with metabolic pathways are those encoding a haloacid dehalogenase (LBJ_RS17075) and a methylmalonyl-CoA mutase (LBJ_RS11290), although these genes appear to have putative paralogs with similar function in the genome.
: evolution's misplaced witnesses.
Key decision nodes depend on whether or not alternate assays (such as unique Sanger sequencing assays that discriminate against pseudogenes
) need to be developed to ensure maximum clinical utility of the test.
(1) Long reads allow scientists to sequence full-length gene alleles and capture important elements such as promoter regions, pseudogenes
, and more.
Among them, nuclear pseudogenes
have been increasingly reported (Lopez et al.
Simultaneously, we also should keep in mind that the shorter COI gene sequences may include paralogous nuclear mitochondrial pseudogenes
(numts) that are apt to induce incorrect inference for phylogenetic relationships (Song et al.
The genomic nucleotide sequences of exons 1 to 9 of the ABCC6 gene were very similar to those of ABCC6 pseudogenes
. In particular, we confirmed that the pseudogenes
contained the nonsense variant c.1132C>T (p.Q378X) in exon 9 even in the Japanese population, as was previously reported .