Sook Jung

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data

The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

BackgroundThe Cotton Microsatellite Database (CMD) http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding.DescriptionAt present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps.ConclusionThe collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

The Genome Database for Rosaceae (GDR): year 10 update

The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.

The high oleate trait in the cultivated peanut [Arachis hypogaea L.]. I. Isolation and characterization of two genes encoding microsomal oleoyl-PC desaturases.

Abstract Plant oils rich in oleate are considered superior products compared to oils rich in polyunsaturated fatty acids. Peanut (Arachis hypogaea L.) is one of the major oilseed crops, and high oleate mutant varieties with as much as 85% oleate have been reported. We examined the possibility that this mutant phenotype resulted from reduction in the activity or the transcript level of microsomal oleoyl-PC desaturase. Two independently generated high oleate mutants, M2-225 and 8-2122, and their partially isogenic lines with a normal oleate phenotype were used in this study. Two cDNA sequences coding for microsomal oleoyl-PC desaturases, ahFAD2A and ahFAD2B, have been isolated from the developing peanut seed with a normal oleate phenotype. Cultivated peanut is an allotetraploid, and sequence comparisons with the genes from the putative diploid progenitor species suggested that ahFAD2A and ahFAD2B are non-allelic, but homeologous genes originating from two different diploid species. Northern analysis showed that the transcripts of oleoyl-PC desaturases are highly abundant in both normal and high oleate peanut seeds in the second stage of development. Differential digestion of the RT-PCR products revealed a restriction site polymorphism between ahFAD2A and ahFAD2B, and allowed us to examine the level of transcript expressed from each gene. The results indicate that ahFAD2A is expressed in both normal and high oleate peanut seeds, but the steady state level of the ahFAD2B transcript is severely reduced in the high oleate peanut varieties. These data suggested that the reduction in ahFAD2B transcript level in the developing seeds is correlated with the high oleate trait.

The high oleate trait in the cultivated peanut [Arachis hypogaea L.]. II. Molecular basis and genetics of the trait

Abstract A peanut variety with high oleate content has previously been described. When this high oleate variety was used in breeding crosses, the F2 segregation ratio of high oleate to normal oleate progeny was 3:1 or 15:1 depending on the normal oleate varieties used in the crosses. These data suggested that the high oleate trait is controlled by two recessive genes, and some peanut varieties differ from the high oleate variety by mutations in one gene, while others differ by mutations in two genes. The objective of this study was to understand the molecular nature of the high oleate trait and the various segregation patterns. In the previous paper in this issue, we reported that the level of transcripts expressed by one (ahFAD2B) of two homoeologous genes for oleoyl-PC desaturases in cultivated peanut is significantly reduced in high oleate varieties. In this report, we examined gene expression by RT-PCR/restriction digestion in a cross that shows a one-gene segregation pattern for the high oleate trait. Our data showed that the severely reduced level of ahFAD2B transcript correlates absolutely with the high oleate phenotype in this cross, suggesting that the single gene difference is correlated with the ahFAD2B transcript level. When we tested the enzyme activity of the proteins encoded by ahFAD2A and ahFAD2B by expression of the cloned sequences in yeast, only the ahFAD2B gene product showed significant oleoyl-PC desaturase activity. These data, combined with the observation that ahFAD2A shows a change (D150N) in a residue that is absolutely conserved among other desaturases, raised the possibility that the ahFAD2A in these normal and high oleate lines is a mutant allele. In support of this hypothesis, we found that another ahFAD2A allele in a normal oleate peanut line does not have the D150N change. This peanut line displays a two-gene-segregation pattern for the high oleate trait. In conclusion, our results suggest that a mutation in ahFAD2A and a significant reduction in levels of the ahFAD2B transcript together cause the high oleate phenotype in peanut varieties, and that one expressed gene encoding a functional enzyme appears to be sufficient for the normal oleate phenotype.

High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.

A high-oleate trait in the cultivated peanut (Arachis hypogaea L.) was reported to rely on the allelic composition of the two homeologous, microsomal oleoyl-PC desaturase genes (ahFAD2A or ahFAD2B). The enzyme activity of either ahFAD2A or ahFAD2B is sufficient for a normal oleate phenotype, and a significant reduction in the levels of ahFAD2B and a mutation in ahFAD2A were reported to be responsible for the high-oleate phenotype in one chemically induced mutant (M2-225) and one derived from a naturally occurring (8-2122) mutant. Here, we report an insertion of the same miniature inverted-repeat transposable element (MITE) in the ahFAD2B gene in another chemically induced mutant (Mycogen-Flavo) and the previously characterized M2-225 mutant. In both cases, this MITE insertion in ahFAD2B causes a frameshift, resulting in a putatively truncated protein sequence in both mutants. The insertion of this MITE in ahFAD2B, in addition to the point mutation in ahFAD2A, appears to be the cause of the high-oleate phenotype in Mycogen-Flavo and M2-225 mutants. Utilizing sequences of the MITE, we developed a DNA marker strategy to differentiate the two insertion-containing mutants from the normal oleate peanut variety (AT-108) and the naturally occurring, high-oleate mutant 8-2122. Reverse transcript-PCR/differential digestion results reveal the expression of both ahFAD2A and ahFAD2B genes in Mycogen-Flavo mutant. This result is in contrast to the observation that ahFAD2B transcripts are greatly reduced in the M2-225 mutant having the MITE insertion further 3′ in ahFAD2B gene.

GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research

BackgroundPeach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools.DescriptionThe Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity.ConclusionsThe GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

CottonGen: a genomics, genetics and breeding database for cotton research

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

BackgroundRosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes.ResultsOur analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes.ConclusionOur analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.