ABSTRACT: An investigation into the genetic diversity of in-farm and gene bank cacao resources in Baracoa Region using SNPs derived from ddRADseq technology.
Project description:The genetic diversity of JEV vaccine strains SA14-14-2, SA14-5-3 and SA14-2-8 and the WT parental WT strain they were derived from, SA14, were sequenced using Illumina technology. Passages of the strains were also sequenced to observe changes in genetic diversity.
Project description:Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. High levels of genetic diversity were observed throughout the 19 E. urophylla populations based on genome-wide SNP data (HE=0.2677 to 0.3487). Analysis with STRUCTURE software, Principal component analysis (PCA) and a neighbor-joining (NJ) tree indicated that E. urophylla populations could be divided into three groups, and moderate and weak population structure was observed with pairwise genetic differentiation (FST) values ranging from −0.09 to 0.074. The low genetic diversity and shallow genetic differentiation found within the 19 populations may be a consequence of their pollination system and seed dispersal mechanism. In addition, 55 core germplasms of E. urophylla were constructed according to the genetic marker data. The genome-wide SNPs we identified will provide a valuable resource for further genetic improvement and effective use of the germplasm resources.
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. MethylC-seq from naturally-occurring Arabidopsis accessions
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation.
Project description:With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity contribute to both attenuation and virulence. The differences in genetic diversity of wild-type Asibi virus and 17D-204 vaccine provides an unique opportunity to investigate RNA population theory in the context of a well described live attenuated vaccine. Utilizing infectious clone-derived viruses containing some of the amino acid substitutions that differentiate yellow fever wild-type Asibi strain from 17D vaccine and recovered in a controlled experiment, establishes that the genetic diversity differences that exist between wild-type Asibi and 17D-204 vaccine viruses are not influenced by either different passage history or source of samples, but rather resulted from the attenuation of wild-type Asibi virus to yield the 17D vaccine sub-strains.
Project description:Investigation of the genetic diversity of Emiliania huxleyi, genomic DNA from 15 different strains were compared with the genomic DNA of the sequenced E. huxleyi strain CCMP1516. Gephyrocapsa oceanica and Isochrysis galbana as phylogenetic closely related taxa were used as out-groups.
Project description:Asian salamander Hynobiidae is commonly observed in the Far East Asia regions, including Korea, Japan, China, and the eastern region of Russia. In Korea, there are four Hynobiidae species known to be lived: Hynobius leechii, Hynobius quelpaertensis, Hynobius yangi, and recently reported Hynobius unisacculus. However, even H. leechii which is broadly colonized in Korea peninsula seems to have a new species candidate, which has distinctive genetic and phenotypic characteristics. Genomic resources are essential to understand the current status of these species, but due to the large size of their genomes (about 16 to 20 Gb), it is not easy to analyze. To reveal the genomic characteristics of these species, we constructed more than ten thousands of protein-coding gene sequences from multiple samples of each species, using the de novo transcriptome assembly approach from RNA-Seq data, confirming their taxonomic relationship which was reported based on mitochondrial DNA and marker genes. Also, by comparing previously reported transcriptome of Hynobius chinensis and Hynobius retardatus, lived in China and Japan, respectively, we found that Korean species have unique genetic signatures. By comparing vertebrate model organism genes, we reported Hynobidaii specific proteins. These data would be a useful resource to study other Caudata species in the future. This research was supported by the National Institute of Biological Resources, Republic of Korea, under the project "Genetic diversity of animal resources” (NIBR201703203 and NIBR201803101).
Project description:Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation and/or allocation. To identify candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations.