Gyoungju Nah

Uncovering the novel characteristics of Asian honey bee, Apis cerana , by whole genome sequencing

BackgroundThe honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana.ResultsUsing de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes.ConclusionsThis first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory.

Validating DNA Polymorphisms Using KASP Assay in Prairie Cordgrass (Spartina pectinata Link) Populations in the U.S.

Single nucleotide polymorphisms (SNPs) are one of the most abundant DNA variants found in plant genomes and are highly efficient when comparing genome and transcriptome sequences. SNP marker analysis can be used to analyze genetic diversity, create genetic maps, and utilize marker-assisted selection breeding in many crop species. In order to utilize these technologies, one must first identify and validate putative SNPs. In this study, 121 putative SNPs, developed from a nuclear transcriptome of prairie cordgrass (Spartina pectinata Link), were analyzed using KASP technology in order to validate the SNPs. Fifty-nine SNPs were validated using a core collection of 38 natural populations and a phylogenetic tree was created with one main clade. Samples from the same population tended to cluster in the same location on the tree. Polymorphisms were identified within 52.6% of the populations, split evenly between the tetraploid and octoploid cytotypes. Twelve selected SNP markers were used to assess the fidelity of tetraploid crosses of prairie cordgrass and their resulting F2population. These markers were able to distinguish true crosses and selfs. This study provides insight into the genomic structure of prairie cordgrass, but further analysis must be done on other cytotypes to fully understand the structure of this species. This study validates putative SNPs and confirms the potential usefulness of SNP marker technology in future breeding programs of this species.

Uncovering the Differential Molecular Basis of Adaptive Diversity in Three Echinochloa Leaf Transcriptomes

Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli.

Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions

Abstract The complete chloroplast (cp) genomes of three Echinochloa crus-galli accessions (KR822684, KR822685, and KR822686) are reported in this work. The cp genome size is similar in three accessions, ranging from 139 846 bp to 139 860 bp. All three genomes have two inverted repeats (IR) of 22 748 bp per each IR with a large single copy (LSC) region of 81 833–81 844 bp and a small single copy (SSC) region of 12 517–12 520 bp. The total of 131 genes was identified in individual accession. Phylogenetic analysis revealed three Korean Echinochloa accessions belonged to E. crus-galli, and diverged less than 0.1 million years ago (Mya).

Dormancy Associated Weedy Risk of the F1 Hybrid Resulted from Gene Flow from Oilseed Rape to Mustard

To assess the dormancy associated weedy risk of the F1 hybrid generated by hybridization between Brassica juncea (maternal) and Brassica napus (paternal), seed germination, dormancy and longevity were examined sequentially after seed harvest. The F1 hybrids exhibited the intermediate characteristics of their parents in seed germination and dormancy with relatively high dormancy rate of 41.1%. In summer, F1 hybrid seeds buried in the 3 cm soil exhibited greater viability (52.4%) than those in the soil surface with greater seed longevity (74.6%) than its maternal (63.3%) and paternal (33.7%) parents at 100 days of over-summering in soil. In winter, F1 seeds buried in the soil surface were more viable than those in the 3 cm soil with greater seed longevity (83.5%) than its maternal (39.0%) and paternal (71.7%) parents at 100 days of over-wintering in soil. Therefore, it is concluded that F1 hybrid resulted from gene flow from OSR to mustard has high seed dormancy and longevity during summer and winter, suggesting its weedy risk potential. Further studies are required to examine the reproductivity and fitness cost of F1 hybrid to make a clearer conclusion of its weedy risk.

Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Single nucleotide polymorphisms (SNPs) play important roles as molecular markers in plant genomics and breeding studies. Although onion (Allium cepa L.) is an important crop globally, relatively few molecular marker resources have been reported due to its large genome and high heterozygosity. Genotyping-by-sequencing (GBS) offers a greater degree of complexity reduction followed by concurrent SNP discovery and genotyping for species with complex genomes. In this study, GBS was employed for SNP mining in onion, which currently lacks a reference genome. A segregating F2 population, derived from a cross between ‘NW-001’ and ‘NW-002,’ as well as multiple parental lines were used for GBS analysis. A total of 56.15 Gbp of raw sequence data were generated and 1,851,428 SNPs were identified from the de novo assembled contigs. Stringent filtering resulted in 10,091 high-fidelity SNP markers. Robust SNPs that satisfied the segregation ratio criteria and with even distribution in the mapping population were used to construct an onion genetic map. The final map contained eight linkage groups and spanned a genetic length of 1,383 centiMorgans (cM), with an average marker interval of 8.08 cM. These robust SNPs were further analyzed using the high-throughput Fluidigm platform for marker validation. This is the first study in onion to develop genome-wide SNPs using GBS. The resulting SNP markers and developed linkage map will be valuable tools for genetic mapping of important agronomic traits and marker-assisted selection in onion breeding programs.

Phylogenetic Relationship of Echinochloa Species Based on Simple Sequence Repeat and Phenotypic Marker Analyses

Echinochloa species are among the most troublesome weeds in rice cultivation, and grow in a broad habitat range in Korea. Although various ecotypes of Echinochloa have been collected as germplasm for future studies, it has been difficult to classify them due to their high level of morphological similarity. This study was thus conducted to develop and investigate the phylogenetic relationships between 77 Echinochloa accessions with the use of 23 simple sequence repeat (SSR) markers and 24 morphological traits. Of 77 Echinochloa accessions, including 57 accessions from Korea and 5 reference species, late watergrass was clearly clustered as a distinctive group from barnyardgrass and other Echinochloa species. In this analysis, we also identified core genetic and morphological markers that can be used for the future identification and classification of Echinochloa species. Five out of 23 SSR makers produced distinctive bands that discriminate late watergrass from barnyardgrass and other Echinochloa species. Four morphological traits of the reproductive organs were the most influential contributors for classifying Echinochloa species. Although there was no clear consensus generated in this study between SSR markers and morphological trait analyses, our results support the potential use of the selected SSR markers and morphological traits in future studies of Echinochloa. Nomenclature: Barnyardgrass, Echinochloa crus-galli (L.) Beauv.; junglerice, Echinochloa colona (L.) Link; late watergrass, Echinochloa oryzicola Vasing; gulf cockspur, Echinochloa crus-pavonis (H. B. K.) Schultes; early watergrass, Echinochloa oryzoides (Ard.) Fritsch.; Echinochloa hispidula (Retz.) Nees ex Royle; Echinochloa muricata (P. Beauv.) Fernald.

Complete chloroplast genomes of two Miscanthus species

Abstract The complete chloroplast (cp) genomes of two Miscanthus species, M. sinensis and M. sacchariflorus, were sequenced and investigated for genes, genome size variation, and polymorphisms. There are 170 genes in both cp genomes, consisting of 122 mRNA genes (84 protein-coding genes and 38 hypothetical genes), 40 tRNA genes, and 8 rRNA genes. The cp genome contains two inverted repeat (IR) regions, separated by large single copy (LSC) region and small single copy (SSC) region. Indels were responsible for 40 bp difference in cp genome size in two species. In addition, we established phylogenetic relationship with other monocot cp genomes, and estimated divergence time. The two Miscanthus species clustered together among other C4 monocot species and the divergence time of two Miscanthus species was approximately 0.5 1–0.84 Mya.

Evaluation of maximum potential gene flow from herbicide resistant Brassica napus to its male sterile relatives under open and wind pollination conditions

Pollen-mediated gene flow (PMGF) from genetically modified (GM) Brassica napus to its wild relatives by wind and insects is a major ecological concern in agricultural ecosystems. This study conducted is to estimate maximum potential gene flow and differentiate between wind- and bee-mediated gene flows from herbicide resistant (HR) B. napus to its closely-related male sterile (MS) relatives, B. napus, B. juncea and Raphanus sativus. Various markers, including pods formation in MS plants, herbicide resistance, and SSR markers, were used to identify the hybrids. Our results revealed the following: 1) maximum potential gene flow (a maximum % of the progeny of pollen recipient confirmed hybrid) to MS B. napus ranged from 32.48 to 0.30% and from 14.69 to 0.26% at 2-128 m from HR B. napus under open and wind pollination conditions, respectively, and to MS B. juncea ranged from 21.95 to 0.24% and from 6.16 to 0.16%, respectively; 2) estimates of honeybee-mediated gene flow decreased with increasing distance from HR B. napus and ranged from 17.78 to 0.03% at 2-128 m for MS B. napus and from 15.33 to 0.08% for MS B. juncea; 3) a small-scale donor plots would strongly favour insect over wind pollination; 4) no gene flow occurred from HR B. napus to MS R. sativus. Our approach and findings are helpful in understanding the relative contribution of wind and bees to gene flow and useful for estimating maximum potential gene flow and managing environmental risks associated with gene flow.