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Col vs Ler Comparison

Alan Rose abrose at UCDAVIS.EDU
Mon Mar 11 15:09:11 EST 1996

Many thanks to all who responded to my question about Col vs Ler sequence
polymorphisms. Most genes from these ecotypes differ by less than 5
nucleotides, but there are a few genes that are quite divergent (up to
nearly 4%). The following are excerpts from the responses.   Alan Rose

Our anectdotal comparison is for the AGL15 gene.  We ended up sequencing
almost the whole coding region, all the introns and a couple hundred bases
of 3'
UTR from three ecotypes (roughly 2 kb in each).  The only differences
we found: a single base transition between WS and Col in the third intron;
a single transition and a single transversion between WS and Ler in the
third intron.  So between Col and Landsberg there is a single transition
and two transversions in the third intron.  Greg Heck

I sequenced a beta-amylase cDNA from a Columbia library:
Then Satoru Mita published the gene sequence that was isolated from Landsberg
erecta: http://www2.ncbi.nlm.nih.gov/cgi-bin/birx_doc?genbank+499604
In their paper (Plant Physiology, 1994, 107:985-904) they mention a single T/G
difference at #2694 of their sequence that changes a Phe to Leu.  Jon Monroe

We have looked in the Bel gene, Cell, vol. 83, 753-742, dec.1 1995.  Nir Ohad

We have cloned the GA5 gene from both Col and Ler ( PNAS, 92:6640). The
accession nos are U20872(ler) and U20873(Col). Both are genomic sequences.
Yun-Ling Xu

I can submit the two examples below: gamma-TIP and Gibberellin 20-oxidase
(GA5). In both cases, a genomic clone from Columbia is compared with a cDNA
from Ler, so the introns are gapped out. Athgtip is the TIP from Columbia,
2122.seq is my sequence for TIP from Ler. ATU20873 is the GA5 gene (GA
20-oxidase) from Col, At2301 is the cDNA of the same gene from Ler. There is
also (I think) a genomic sequence for GA5 from Ler in the database
(ATU20872?).   Andy  Phillips

I have almost completed the sequencing of a genomic clone of a
calcium-dependent protein kinase from both Landsberg erecta and Columbia
and have found no differences in sequence as yet (even in the introns).
Estelle M. Hrabak

We described the differences in the Columbia and Landsberg chalcone
synthase genes in Plant J. 8(5)" 659-671 (1995).  There were two
differences in about 1400 nt, one in the untranslated leader and a second,
silent, change in the second exon (open boxes in Figure 5). Brenda W. Shirley

I have sequenced two genes from Col and Ler, LFY and UFO.  LFY has a
single (silent) mutation, while UFO has a single mutation that makes for
a non-conservative aa change.  Detlef Weigel

When RPS2 was sequenced from both Columbia and Landsberg, only one base
change was found, which conveniently made a Sau3A polymorphism.  If you
look at the original CAPS paper (Konieczny and Ausubel 1993 Plant Journal
4:403-410) that may help a bit.  It has some estimates of the frequency
with which polymorphisms occur between the two ecotypes. Jane Glazebrook

I don't have the sequence comparisons in front of me, but you may want to
compare the sequences of the A subunit of protein phosphatase 2A from
Landsberg and Col.  The accession numbers are:  X82001 (REGA of Slabas et
al.), ATU21557 (our RCN1 cDNA sequence) and ATU27299 (an identical cDNA seq
from Sabine Rundle et al.).  The X82001 seq is a genomic clone isolated
from "Landsberg" whether this is _Ler_ or not I can't say; the other two
clones come from Col. The Col and Landsberg PP2A-A sequences are at least
99% identical--I think only three or four amino acid differences (one K/E
diff, one G/E diff, one Y/D diff, and one two amino acid insertion [AA]
that I'm a bit sceptical about).  There are a few silent nucleotide
differences in the coding sequence, and in regions where I've compared
intron and upstream sequences there are a few more changes.  There are also
two other A subunit isoforms published by Slabas et al. (X82003 and
X82003), but those sequences are clearly different from the RCN/REGA PP2A-A
subunit.  Alison DeLong

We sequenced the cDNA and genomic sequence of lipoxygenase 1 (LOX1) from
Col and Lands respectively.  The coding sequence  and UTRs were identical
for both but I suspect that there may be some upstream and intron
differences between the two ecotypes. References are:  cDNA - Melan, et al.
1993. Plant Physiol. 101: 441-450. genomic - Melan et al. 1994. Biochim.
Biophys Acta. 1210: 377-380. Melissa Melan

The LTP1 promoter region was determined from both columbia and ler.
The columbia sequence is in the database as m80567. As I recall, there were
significant differences in the sequence. Chris Somerville

Out of 2627 bp of the single-copy PAT1 gene, the Col and Ler sequences
differ at 88 nucleotides and there are 11 insertions/deletions. These cause
9 amino acid differences, but 7 of these are in the plastid transit
peptide, and the remaining 2 differences are chemically conservative
changes in phylogenetically non-conserved residues. The TSA1 gene differs
in 4 out of 3072 bp, but 3 of these are in 5' flanking sequences. As
mentioned in the original CAPS mapping paper (Konieczny and Ausubel 1993,
Plant J. 4:403-410) "the ADH locus contains 10 bp changes between Ler and
Col concentrated in a 220 bp region, but only 13 total changes within a
total of 2900 bp". That paper also estimates "that on average, Ler and Col
genes differ once in every 261 bp".  Alan Rose

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