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Prunus yedoensis (P. yedoensis) is a popular flowering species that is appreciated worldwide. While there are very few genetic variations among the planted populations of this species that are considered cultivated, diverse variations have been found in natural wild cherry populations on Jeju Island. In this study, we assembled a consensus reference chloroplast DNA (cpDNA) sequence with an aim to build a standard reference sequence of cpDNA to study genetic diversity and to characterize individual lines with the DNA barcoding technique in P. yedoensis. Full cpDNA was sequenced using the Illumina high-throughput DNA sequencing platform (HiSeq2500). Standard cpDNA sequences of P. yedoensis were obtained based on the four collected samples and two previously reported cp genome sequences from the NCBI. The sequenced cp genome consisted of 131 genes, of which 37 encoded tRNAs, 8 encoded rRNAs and 86 encoded proteins. There were 17 duplicated genes, including 4 rRNA genes, 7 tRNA genes and 6 protein-coding genes, with an overall GC content of 36%. When compared with the reference genome, 66 SSRs, 168 SNPs and 531 INDELs were identified within the 4 individual samples. These divergences comprising SSR, SNP and INDEL markers will be useful for testing the maternal inheritance of the chloroplast genome, for detecting species differentiation and even for breeding programs. Standard whole cp sequences were successfully assembled, resulting in a good resource to develop DNA barcodes, which will facilitate studies on genetic diversity, evolution, origins and cultivar-specific marker development. [ABSTRACT FROM AUTHOR]

Background: Euphorbia jolkini, a medicinal herb that grows on the warm beaches in Japan and South Korea, is known to be used for traditional medicines to treat a variety of ailments, including bruises, stiffness, indigestion, toothache, and diabetes. Objective: It is to analyze the whole transcriptome and identify the genes related to the phenylpropanoid biosynthesis in the medicinally important herb E jolkini. Methods: Paired-end Illumina HiSeq™ 2500 sequencing technology was employed for cDNA library construction and Illumina sequencing. Public databases like TAIR (The Arabidopsis Information Resource), Swissprot and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used for annotations of unigenes obtained. Results: The transcriptome of E. jolkini generated 139,215 assembled transcripts with an average length of 868 bp and an N50 value of 1460 bp that were further clustered using CD-HIT into 93,801 unigenes with an average length of 847 bp (N50-1410 bp). Sixty-three percent of the coding sequences (CDS) were annotated from the longest open reading frame (ORF). A remarkable percentage of unigenes were annotated against various databases. The differentially expressed gene analysis revealed that the expression of genes related to the terpenoid backbone biosynthesis pathway was higher in the flowers, whereas that of genes related to the phenylpropanoid biosynthesis pathway was both up- and downregulated in flowers and leaves. A search of against the transcription factor domain found 1023 transcription factors (TFs) that were from 54 TF families. Conclusion: Assembled sequences of the E. jolkini transcriptome are made available for the first time in this study E. jolkini and lay a foundation for the investigation of secondary metabolite biosynthesis. [ABSTRACT FROM AUTHOR]

Background: Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. Dwarfism in plants prevents lodging and therefore it's a desired trait in crops. Objective: To find differentially expressed genes to classify and understand the regulation of genes related to plant growth in mutant dwarf soybeans, which appeared in the F5 generation. Methods: We obtained a few segregated dwarf soybeans in the populations derived from the crossing of Glycine max var. Peking and Glycine soja var. IT182936 in an F5 RIL population. These dwarf soybeans may be useful genetic resources for plant breeders, geneticists and biologists. Using the Illumina high-throughput platform, transcriptomes were generated and compared among normal and dwarf soybeans in triplicate. Conclusion: We found complex relationship of the expressed genes to plant growth. There were highly significantly up-/downregulated genes according to the comparison of gene expression in normal and dwarf soybeans. The genes related to disease and stress responses were found to be upregulated in dwarf soybeans. Such over-expression of disease resistance and other immune response genes can be targeted to understand how the immune genes regulate the response of plant growth. In addition, photosynthesis-related genes showed very low expression in dwarf lines. The transcriptome expression and genes classified as related to plant growth may be useful resources to researchers studying plant growth. [ABSTRACT FROM AUTHOR]

The Betulaceae family comprises two subfamilies, Betuloideae and Corylaceae. The subfamily Betuloideae contains two genera, Alnus Mill. and Betula L. Twenty putative long terminal repeat (LTR) retrotransposons were mined from 171 scaffolds containing 5,208,995 bp of dwarf birch (Betula nana) genome sequences. Five retrotransposons were finally selected after filtering the retrotransposon canonical features and nucleotide similarities between left and right LTR sequences. Of the five retroelements, three elements were found to be Ty1/Copia retrotransposons; identity of the other two elements could not be ascertained due to sequence undetermined ‘N’ bases in the sequence database. Inter-retrotranposon amplified polymorphism (IRAP) analysis, based on the LTR sequences of the mined LTR-retrotransposons, produced 179 discernible IRAP bands among the Alnus and Betula genera. Sequence analysis revealed no size homoplasy among the homologous IRAP bands. Phylogenetic and principle coordinate analysis, based on the band sharing among the taxa, showed the species in two different genera were clearly separated. The subgenera in each genus of Alnus and Betula were also distinguishable from the IRAP profiles. In the genus Betula, the species in subgenus Betula showed mixed clustering between species. This is incongruent with the phylogeographical distribution of the species. [ABSTRACT FROM AUTHOR]

Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm. [ABSTRACT FROM AUTHOR]

Several members of the genus Sterculia have a great potential as a candidate for the identification of new drug lead molecules, but lack of their genomic information can be a hindrance for the verification of the genetic background for future use. To obtain genomic resources, RNA-seq transcriptome analysis was conducted using leaves of Sterculia lanceolata, a member of the genus Sterculia, resulting in a total of 28,088,794 clear reads with a length of 3,692,930,973 bp. De novo assembly generated 7857 (3,559,905 bp) non-redundant unigenes with an average length of 453 bp. Among 1893 unigenes assigned by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) database, a total of 1158 were mapped into 328 different metabolic pathways. The biosynthesis of secondary metabolites (KO01110) pathway was the second highest hits with 159 unigenes, of which 72 are known to be involved in terpenoid, phenylpropanoid, and flavonoid biosynthesis. The search for simple sequence repeats (SSRs) identified a total of 899 SSRs. Nineteen polymorphic SSR markers were developed, of which polymorphism information content (PIC) values ranging from 0.10 to 0.49. Both Principal Coordinates Analysis (PCoA) and neighbor joining analysis using allelic data formed three clusters among 15 Sterculia species. The cluster of genotypes formed in the PCoA shows the genotypes in close proximity to those in neighbor joining tree. Taken together, our results provide a valuable source for genetic studies and also for molecular studies to unravel underlying mechanisms involved in medicinal properties of Sterculia L. [ABSTRACT FROM AUTHOR]