Title of article :
Status of SSR, cSSR, iSSR and VNTR motifs in Leptosphaeria maculans based on high throughput sequencing data
Author/Authors :
Zamanmirabadi, A Department of Plant Protection - Faculty of Agriculture - University of Zanjan, Zanjan, Iran , Hemmati, R Department of Plant Protection - Faculty of Agriculture - University of Zanjan, Zanjan, Iran , Dolatabadian, A Department of Plant Science - University of Manitoba - Winnipeg - MB R3T 2N2 - Canada UWA School of Biological Sciences and the UWA Institute of Agriculture - Faculty of Science - The University of Western Australia, Crawley, WA, Australia
Abstract :
Leptosphaeria maculans is a fungus of
the phylum Ascomycota that is a causal agent of
blackleg disease on canola (Brassica napus L.). Due
to the high diversity and worldwide distribution, L.
maculans has been widely studied as a model
phytopathogenic fungus. Simple sequence repeats
(SSRs) are robust molecular markers widely used
for population diversity research. This study utilized
whole-genome sequencing data of four Iranian L.
maculans isolates (Pk4, Ar3, Ar5, and Alam10). We
compared them with the JN3 reference genome to
identify and compare different types of SSRs,
including perfect (SSRs), compound (cSSR),
imperfect (iSSR) and variable tandem number
repeats (VNTR) motifs. The average length of SSRs
was estimated to be 155.692 kb, accounting for
0.36% of the total genome. An average of 7138 SSR
motifs with a frequency of one SSR per 169.5 bp,
including an average of 33.86% tri, 25.69% di,
14.48% mono, 10.87% tetra, 8.52% hexa, 6.58%
penta-nucleotide repeats, were identified from
assembled genomic sequences. Of the total SSRs
identified in the Pk4 isolate, 459 motifs were
identified in CDS regions. Approximately 13% of
the identified SSRs were linked to cSSRs. The
average cSSR loci density for four isolates was
487.32 bp/Mb, and C, AG and AC were the most
frequent SSR motifs. The assessed isolates' cSSRs
lengths ranged from 24 to 295 bp. The largest
common cSSRs in four isolates were identified as a
motif (GA)26-(CAGAGA)15 with a length of 142 bp.
The tri-nucleotide (AAT) was the most common
iSSRs motif, followed by di, tetra, mono, hexa, and
penta-nucleotides. About 30% of iSSRs contained
the AAT, AT, and AAG motifs. Among the 7 to 30
nucleotide motifs, 7, 8, 9, and 10 motifs showed the
most occurrences. In addition, 11 motifs with more than 100 nucleotides were found in the studied
isolates and the reference genome. The data
demonstrate that these results can be used to
characterize L. maculans isolates from diverse hosts
and geographic locations and are transferable to
other isolates of L. maculans.
Keywords :
Blackleg , SSRs , Leptosphaeria maculans , NGS
