Genome-wide analysis of microsatellite sequence in seven filamentous fungi
Abundance of microsatellites with repeated unit lengths of 1-6 base pairs in seven fungi: Aspergillus nidulans, Coprinus cinereus, Cryptococcus neoformans (serotype A), Fusarium graminearum, Magnaporthe grisea, Neurospora crassa and Ustilago maydis were investigated on genomic scale. The results sho...
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Published in | Interdisciplinary sciences : computational life sciences Vol. 1; no. 2; pp. 141 - 150 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Springer
International Association of Scientists in the Interdisciplinary Areas
01.06.2009
Springer Nature B.V |
Subjects | |
Online Access | Get full text |
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Summary: | Abundance of microsatellites with repeated unit lengths of 1-6 base pairs in seven fungi:
Aspergillus nidulans, Coprinus cinereus, Cryptococcus neoformans
(serotype A),
Fusarium graminearum, Magnaporthe grisea, Neurospora crassa
and
Ustilago maydis
were investigated on genomic scale. The results showed that each species has its specific profile for different types and different motifs of SSR loci. Ascomycetes fungi
M. grisea, N. crassa
and basidiomycete fungus
U. maydis
adopt much more microsatellites than other fungi examined. Total amount of 15,751, 14,788 and 6,854 SSR loci were observed respectively, average density is 406, 389 and 347 per Mbp sequence; overall length of SSR sequence was 0.82%, 0.95% and 0.79% of genomic sequence respectively. While ascomycetes fungus
F. graminearum
and
A. nidulans
contains the least SSRs in the genomic DNA, only 4,679 and 4,837 tracts were observed in 36 Mb and 30 Mb genomic sequence respectively. Microsatellite repeats in protein coding regions are investigated in
Aspergillus nidulans, Magnaporthe grisea
, and
Neurospora crassa
also, the results show that the difference of different types and motifs among three fungi is very little than that in whole genomic sequence. For trinucleotide repeats, overrepresent (comparing to the total base pair of protein coding region) of AGC, GGC, AGG, ACG and ACC was observed in coding region, frequencies of AAC and AAG were not difference between coding and non-coding region, AAT, AGT and ATG were underrepresent in coding region excepted for
A. nidulans
, in which ATG was overrepresentative. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 |
ISSN: | 1913-2751 1867-1462 |
DOI: | 10.1007/s12539-009-0014-5 |