Recent increase of raw sequences generated by next generation sequencing (NGS) machines enabled re-analyzing raw sequences for diverse purposes: one is assembling organelle genome. One recent study completed the mitochondrial genomes of 14 ants from public raw sequences in subfamily Pseudomyrmecinae not having organelle genomes. Along with this approach, we have found four ant species of which genome papers were published and its raw sequences were open to public but its mitochondrial genome has not been assembled yet: Harpegnathos saltator and three Pogonomyrmex species (P. rugosus, P. anergismus, and P. colei). We assembled four complete mitochondrial genomes, presenting mitogenome of H. saltator 16,467 bp long and those of three Pogonomyrmex species above 21 kb long, ranking top among all known Hymenopteran mitogenomes. Four mitochondrial genomes contain 13 PCGs, 22 tRNAs, and 2 rRNAs, conserved as in all other insects. Phylogenomic tree based on partial or complete mitogneomes covering 26 genera provides insights of ant mitogenomic phylogeny and evolution.

Due to rapid increase of international trade, many invasive and exotic pests have been introduced in Korea. One of typical example is Solenopsis invicta found in harbor and nearby areas unexpectedly triggering alerts of invasive and exotic pests. Practically, critical limitation to identify these species based on morphology exists because of lack of experts, so that it is very important to develop fast and accurate methods to identify these species. Molecular marker is one of candidates for satisfying these requirements of invasive and exotic pests: usually COI gene has been used for identifying insect species efficiently. Here, we developed web-based integrated platform for identifying invasive and exotic pests. As a first step, we collected 71,146 COI sequences from 529 species which are potentially invasive and exotic pests in Korea. In addition, we are collecting their complete mitochondrial genome sequences for evaluating additional marker regions which can be more effective for identifying species. Web-based interfaces are under development to access these raw data as well as bioinformatic analysis function to identify species based on mitochondrial sequences. Our platform will be a fundamental resources not only to identify invasive and exotic pests effectively but also to understand ecology of these species to find anticipative policies to prevent invasion of these species.

Nilaparvata lugens, brown planthoppers, is one of important pests on rice. Korean N. lugens is migrated from China and causing severe damages on rice in early September in Korea. For identifying biotypes of these N. lugens based on complete mitochondrial genomes, we completed mitochondrial genome of N. lugens captured in Hadong-gun, Gyoungsang-nam province in Korea. The circular mitogenome of N. lugens is 17,610 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 2,424 bp. The base composition was AT-biased (89.5%). 112 single nucleotide polymorphisms (SNPs) and 59 insertions and deletions are identified by comparing with Chinese N. lugens. Based on phylogenetic trees together with those of N. lugens captured in China, no clear phylogenetic relationship along with five biotypes, requiring more researches to achieve biotype identification including detailed analysis of sequence variations on mitochondrial genomes and whole genome analysis of N. lugens in near future.

The genus Camponotus Mayr, 1861 distributes all over the world, even ranging from the African desserts to the Antarctic islands. Number of species in this genus is the largest: 1,488 taxa (species and subspecies) accounting for 10% ant species. Despite of it, number of available complete mitochondrial genomes was only one, Camponotus atrox (subgenus Camponotus). To decipher characteristics of mitochondrial genome of this genus, we completed mitochondrial genomes of Camponotus nipponensis Santschi, 1937, belonging to subgenera Myrmentoma using Illumina HiSeqX. The total length of mitochondrial genome of C. nipponensis is 15,532bp with 79.8% A + T content. It consists of 13 PCGs, 22 tRNA, and 2 rRNA genes and an A+T–rich control region. This mitochondrial genome will be a useful resource to understand features of Camponotus genus with adding more mitochondrial genomes of other subgenera, such as Paramyrmamblys.

Cost for plant survey has been dramatically reduced due to the development of mobile technology to obtain pictures with their GPS coordination. We developed a PlantGPS system consisting of an Android application specialized for collecting plant pictures and their locations using mobile devices, a server-side component for uploading data, and a web-based interface for managing and analyzing data. As examples of application of our PlantGPS system, surveys of “plants in Nangsae (Daksum) Island” and “ferns in Chollipo arboretum” were conducted. Results showed that our PlantGPS system could be used to quickly survey plant distribution in restricted area with reasonable time and effort.

The IMGD (Insect Mitochondrial Genome Database; http://www.imgd.org) archives 113,985 partially sequenced hexapod mitochondrial genome entries (PMEs), providing various information such as the number of mitochondrial genes or taxonomic information. The 113,985 PMEs show most PCGs including much larger number of PMEs than rRNAs and tRNAs, and the family, genus, and species information are focused on five orders, Coleoptera, Diptera, Lepidoptera, Hymenoptera, and Hemiptera in 31 hexapoda orders. The alignment of 58,238 COI gene entries shows discordance in fragment length and portion, resulting DNA barcode using 5′-region cannot be applied for all COI gene entries overall hexapod orders.

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

Magnaporthe oryzae is a causal pathogen of the rice blast, the most destructive disease of rice worldwide. This ascomycete fungus has been intensively studied as a model organism in plant-pathogen interactions. Recently, the genome sequence of M. oryzae 70-15 was published by International Rice Blast Consortium. This led us to investigate comparative and functional analysis of this pathogen at genome-wide level. As a first step, sequencing project of M. oryzae Korean strain KJ201 was launched to face practical interests on diversity of plant pathogens. We constructed a fosmid library with a copy number controllable pCC1 vector. Over 13,000 end reads from 6637 fosmid clones were generated and anchored on genome sequence of the strain 70-15. Currently, 9,793 end reads, in which 2.684, clones with both ends and 1,757 clones with on end matched, are aligned to the sequence of strain 70-15. In the next step, shotgun sequencing of fosmid clones was conducted for fine scale comparative analysis of chromosome 7 that is well defined in genome sequencing of 70-15. Totally 119 fosmid clones were pooled in region and analyzed. For reasonable intra-species comparison in genome of M. oryzae, two strains, KJ201 and Guy11, were chosen for whole genome shotgun sequencing analysis with GS454 FLX system. About 8X genome coverage sequences were obtained for each strain and being merged for comparative analysis. Genome information of other strains is being also available from China and Japanese research groups and could be joined together for extended comparative analysis and the results give more detail in genome diversity in species level.