Abstract: Background: Small non-coding RNAs (21 to 24 nucleotides) regulate a number of developmental
processes in plants and animals by silencing genes using multiple mechanisms. Among these, the
most conserved classes are microRNAs (miRNAs) and small interfering RNAs (siRNAs), both of
which are produced by RNase III-like enzymes called Dicers. Many plant miRNAs play critical roles
in nutrient homeostasis, developmental processes, abiotic stress and pathogen responses.
Currently, only 70 miRNA have been identified in soybean.
Methods: We utilized Illumina’s SBS sequencing technology to generate high-quality small RNA
(sRNA) data from four soybean (Glycine max) tissues, including root, seed, flower, and nodules, to
expand the collection of currently known soybean miRNAs. We developed a bioinformatics
pipeline using in-house scripts and publicly available structure prediction tools to differentiate the
authentic mature miRNA sequences from other sRNAs and short RNA fragments represented in
the public sequencing data.
Results: The combined sequencing and bioinformatics analyses identified 129 miRNAs based on
hairpin secondary structure features in the predicted precursors. Out of these, 42 miRNAs
matched known miRNAs in soybean or other species, while 87 novel miRNAs were identified. We
also predicted the putative target genes of all identified miRNAs with computational methods and
verified the predicted cleavage sites in vivo for a subset of these targets using the 5’ RACE method.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix
atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a
whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a
chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and
similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted
genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic
recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated
genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene
diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate
the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Background: Phaseolus vulgaris (common bean) is the second most important legume crop in the
world after soybean. Consequently, yield losses due to fungal infection, like Uromyces appendiculatus
(bean rust), have strong consequences. Several resistant genes were identified that confer
resistance to bean rust infection. However, the downstream genes and mechanisms involved in
bean resistance to infection are poorly characterized.
Results: A subtractive bean cDNA library composed of 10,581 unisequences was constructed and
enriched in sequences regulated by either bean rust race 41, a virulent strain, or race 49, an
avirulent strain on cultivar Early Gallatin carrying the resistance gene Ur-4. The construction of this
library allowed the identification of 6,202 new bean ESTs, significantly adding to the available
sequences for this plant. Regulation of selected bean genes in response to bean rust infection was
confirmed by qRT-PCR. Plant gene expression was similar for both race 41 and 49 during the first
48 hours of the infection process but varied significantly at the later time points (72–96 hours after
inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive
response in the bean plants. A biphasic pattern of gene expression was observed for several genes
regulated in response to fungal infection.
Conclusion: The enrichment of the public database with over 6,000 bean ESTs significantly adds
to the genomic resources available for this important crop plant. The analysis of these genes in
response to bean rust infection provides a foundation for further studies of the mechanism of fungal
disease resistance. The expression pattern of 90 bean genes upon rust infection shares several
features with other legumes infected by biotrophic fungi. This finding suggests that the P. vulgaris-
U. appendiculatus pathosystem could serve as a model to explore legume-rust interaction.
