Genes of Tn7 and of Tn7-like transposons carrying a CRISPR-Cas system
Source:R/data.R
tn7_crispr_elements.RdThe genes of Tn7, of Tn6022 and of fourteen Tn7-like transposons that have
picked up a minimal CRISPR-Cas system, which has lost the genes needed to acquire
spacers and to cut the target and is thought to guide the transposon to its
insertion site instead. Each element is drawn from its right end, next to
the gene it inserted beside, so that tnsA is at the left. The elements,
the genomes they sit in and the insertion sites are those of Table S1 and
Fig. 3 of the reference below, and the rows are named after the TnsA tree
node that figure labels them with. Each region starts at the insertion
site and ends at the left end of the element or after the cas genes, as in
that figure. Only the first part of each element is
covered, up to the end of the cas genes; the longer elements carry further
cargo beyond it. Made by data-raw/tn7_crispr_elements.R.
Format
A data frame with 307 rows and 13 columns:
- cluster
Name of the element, as in Fig. 3 of the reference. A character vector.
- strain
Species and strain the element was found in. A character vector.
- strain_short
The strain with its genus abbreviated, e.g. "V. cholerae VC35", for short labels. A character vector.
- accession
Accession of the sequence the region comes from. A character vector.
- site
Gene the element has inserted next to, e.g. "glmS", "yciA" or "SRP-RNA". A character vector.
- locus_tag
Locus tag of the gene. A character vector.
- gene
Gene name, or "" when the gene has none; "R" or "L" for the right or left end of the element, and "CRISPR" for a CRISPR array. A character vector.
- label
The name Fig. 3 of the reference writes on the gene, or "" when it names none: the transposition and cas genes, the insertion sites in short (e.g. "glmS" for "attTn7 (glmS)") and the resistance genes and integrase of Tn7. A character vector.
- product
Description of the gene product. A character vector.
- category
Role of the gene, e.g. "tnsA", "tniQ / tnsD", "cas8f / cas5f", "CRISPR array", "insertion site", "right end" or "left end". A character vector.
- start
Start position of the gene in the region. A numeric vector.
- end
End position of the gene in the region. A numeric vector.
- strand
Strand of the gene, "forward" or "complement". A character vector.
Source
GenBank accession CP076807, RefSeq accession NZ_KB849325 and the
RefSeq genomes of Table S1 of the
reference, read with read_gbk(). The CRISPR arrays that RefSeq does not
annotate were found from the repeat consensus of the type I-F arrays these
elements carry.
Details
Tn7 itself carries tnsE and no cas genes. It is taken from the chromosome
of Acinetobacter baumannii UC20804, where it sits at its insertion site
attTn7, next to glmS; this Tn7 is 99.9% identical over its whole length
to the Tn7 of GenBank DQ176450. Tn6022 is
the other element without cas genes; it sits inside yifB (comM), which
the annotation splits in two, and only the fragment at its right end is kept
here. Its ends are the window between those two fragments and are not
verified to the base. In element
#2757 tnsA is fused to tnsB: the annotated gene is longer than the tnsB
of Tn7 by about the size of a TnsA, and that extra length at its start is
given as a separate row, with gene name "tnsA (fused)" and label "tnsA". The
boundary between the two is an estimate.
Besides the genes, each element has a row for its right end (gene R,
category "right end") and its left end (gene L, category "left end").
Both are single positions, with start equal to end. The left end of most
elements lies far beyond the last gene covered here (up to about 100 kb), at
its true position. Genes that run on past the left end are cut off there.