Open AccessGenomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis
Author(s) -
Estep Matt C.,
Gowda Bhavani S.,
Huang Kan,
Timko Michael P.,
Bennetzen Jeffrey L.
Publication year - 2012
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2011.11.0031
Subject(s) - biology , retrotransposon , genome , tandem repeat , striga , phylogenetic tree , genome size , parasitic plant , genetics , botany , evolutionary biology , transposable element , host (biology) , gene , germination
Generation of ∼2200 Sanger sequence reads or ∼10,000 454 reads for seven Striga Lour. DNA samples (five species) allowed identification of the highly repetitive DNA content in these genomes. The 14 most abundant repeats in these Striga species were identified and partially assembled. Annotation indicated that they represent nine long terminal repeat (LTR) retrotransposon families, three tandem satellite repeats, one long interspersed element (LINE) retroelement, and one DNA transposon. All of these repeats are most closely related to repetitive elements in other closely related plants and are not products of horizontal transfer from their host species. These repeats were differentially abundant in each species, with the LTR retrotransposons and satellite repeats most responsible for variation in genome size. Each species had some repetitive elements that were more abundant and some less abundant than the other Striga species examined, indicating that no single element or any unilateral growth or decrease trend in genome behavior was responsible for variation in genome size and composition. Genome sizes were determined by flow sorting, and the values of 615 Mb [ S. asiatica (L.) Kuntze], 1330 Mb [ S. gesnerioides (Willd.) Vatke], 1425 Mb [ S. hermonthica (Delile) Benth.] and 2460 Mb ( S. forbesii Benth.) suggest a ploidy series, a prediction supported by repetitive DNA sequence analysis. Phylogenetic analysis using six chloroplast loci indicated the ancestral relationships of the five most agriculturally important Striga species, with the unexpected result that the one parasite of dicotyledonous plants ( S. gesnerioides ) was found to be more closely related to some of the grass parasites than many of the grass parasites are to each other.