The genus
Allium
is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new
Allium
species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of
Allium
. We sequenced and assembled four
Allium
chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot
Acorus americanus
to
Allium
, identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the
Allium
species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus
Allium
.
In this study, we investigated differential gene expression in the flower buds of male-fertile and male-sterile pools by using the cDNAsequence-related amplified polymorphism (SRAP) method and discovered a fragment that was specifically expressed in male-fertile pool. Cloning and sequence analysis revealed that this differentially expressed sequence corresponded to a pectin methylesterase gene in Allium cepa (AcPME). This sequence was deposited in GenBank (GU384209). In male-fertility-restored line, AcPME was specifically expressed in tiny buds but not in roots, leaves and bulbs. In malesterile line and maintainer line, AcPME was not expressed in roots, leaves, bulbs or tiny buds. AcPME was differentially expressed during different flowering stages (I, II, III, IV and V). We developed a PCRbased marker (WHR240) associated with the expression of AcPME. This marker was validated in six other onion lines; in each case, the male-fertility-restored onion was reliably identified. WHR240 therefore permits the efficient marker-assisted selection of maintainer individuals in onion breeding programmes.
The RT PCR and RACE methods were used to obtain the cDNA sequence of an APX gene of muskmelon after the leaves were induced with powdery mildew. The cDNA length of the APX gene is 1,047 bp with a 750 bp ORF encoded a 249 amino acid and the molecular weight of APX protein is 27.3 kDa. The analysis showed that the CmAPX genomic DNA contained 10 extrons and 9 introns. The identity of the amino acid sequence deduced from the cDNA with the APX family of other homologous members was about 74-97%. A Full-length of ORF was sub-cloned into prokaryotic expression vector pET24a. The recombinant proteins had high expression level in E. coli. Analysis of expression at mRNA level showed that CmAPX exhibited highly tissue-specific patterns of expression. The mRNA level and enzyme activities assays showed that CmAPX might play an important role in the pathogenesis of powdery mildew.
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