Endosymbionts are important for insect species as they provide essential substances to the host. Due to the technical advance of NGS technology and de novo assemblers, many endosymbionts bacterial genomes are available now. Here, we analysed fourteen endosymbiont bacterial genomes of Aphis genius, one of notorious pest species. Fourteen genomes displayed the length between 628,098 bp to 634,931 bp; GC ratio was from 24.2 % to 25.6 % with no structural variation found. The nucleotide diversity distribution across the 14 endosymbiont genomes revealed three distinct regions, each separated by varying levels of nucleotide diversity. Intraspecific variations identified from endosymbiont bacterial genomes of the same host species revealed numbers of SNPs ranging from 31 (0.0049%) to 1,652 (0.26%) and those of INDELs ranging from 7 (21 bp; 0.0033%) to 104 (285 bp; 0.0045%). 250 unique SSRs, 28 different common SSR groups, and one different SSR group in two genomes were identified and used as a potential molecular marker to distinguish intraspecific population. Phylogenetic analysis further showed congruence between the endosymbiont bacterial genomes and the host species phylogeny, except Aphis nasturtii, Aphis helianth, and Aphis auranti, which require additional endosymbiont genomes for clarification. This comparative analysis result could serve as a cornerstone for understanding the relationship between host and endosymbiont species from a genomic perspective.

Aphis glycines Matsumura, 1917 is a significant agricultural pest worldwide, responsible for the damages to soybeans. In this study, we have assembled three mitogenomes of A. glycines based on the public next-generation sequencing raw reads generated for the whole genome project. Phylogenetic analysis revealed that one of the A. glycines mitogenomes (partial genome; KT889380) was misidentified. Intraspecific variations identified from four aphid species, Aphis glycine, Aphis gossypii, Aphis craccivora, and Myzus pericae mitogenomes exhibited that A. glycines mitogenomes contained a small number of single nucleotide polymorphisms (SNPs) but a large coverage of insertions and deletions (INDELs). In addition, nad2 and nad3 of the A. glycines mitogenomes presented the largest number of SNPs among genes. Various structural variations of transfer RNAs in the three species were investigated. Nucleotide diversity analysis of each gene displayed the same trend between Aphis and Aphididae mitogenomes. Identification and comparison of simple sequence repeats (SSRs) from A. glycines mitogenomes showed that meaningful variations of SSRs were found in the repeat region between nad3 and nad5. Consequently, the observed intraspecific variation within Aphididae species, including A. glycine, can be leveraged to develop molecular markers that facilitate the distinction of populations within species.

The genus Agrimonia L. (1753) is a small group consisting of 19 species and three varieties. We completed two Agrimonia chloroplast genomes, Agrimonia coreana Nakai and Agrimonia nipponica Koidz, collected in Korea and conducted comprehensive analyses of six Agrimonia chloroplast genomes. Two of the Agrimonia chloroplasts genomes have a typical quadripartite structure with lengths ranging from 155,161 bp to 151,362 bp, similar to the remaining AAgrimonia chloroplast genomes. High nucleotide diversity was detected in the ycf1 gene, which can serve as a molecular marker. Intraspecific variations of four A. pilosa chloroplast genomes and interspecific variations of three Agrimonia species revealed that KY419942 is distinct to the other three A. pilosa chloroplast genomes. A phylogenetic analysis demonstrated that KY419942 was clustered with A. nipponica, requiring further analyses to understand Agrimonia species in East Asia. A comparison of simple sequence repeats identified from the six Agrimonia chloroplast genomes suggests potential molecular markers to distinguish species or populations of the same species. Our results define the phylogenetic relationship of three Agrimonia species and provide insight into the intraspecific features of Agrimonia chloroplast genomes with which to gain a better understanding of the genetic structure of Agrimonia species.

In this study, we designed a flexible online teaching environment (On-Flex Teaching) that allows military adult learners, who have greater difficulties in securing study time regularly than ordinary office workers, to participate in their studies on their own initiative. Their academic participation and academic performance were analyzed through analysis of variance and mediation model analysis. As a result of the analysis, in a flexible online learning environment, the group that implemented the pre-study plan performed more learning activities such as downloading lesson plans, answering class questions, and self-evaluation and had higher academic achievement scores than the group that did not follow the plan. Students who performed flexible, self-directed learning activities by flexibly changing the exam time to suit their own circumstances showed higher academic achievement scores through downloading lesson plans and self-evaluation than the group that followed a prior evaluation plan. In addition, as a result of analyzing the mediation model to determine whether the level of self-directed student participation influences the relationship between the degree of implementation of prior study plans and academic achievement, the results showed that establishing study plans increased self-evaluation scores (p<.001) and downloading lesson plans by increasing the number (p<.05), it was found to have a statistically significant positive effect on the total score. Through these results, this study shows that a self-directed, flexible online teaching environment that enables self-directed learning for military adult learners increases students' class participation behavior, As a result, the significance can be found in the fact that major factors that have a positive impact on academic achievement were identified.

In this study, we determined the complete mitochondrial genome of the invasive insect species Melanoplus differentialis captured in Korea. The complete mitochondrial genome of M. differentialis is 15,625 bp long and comprises 13 protein‐coding genes, two ribosomal RNA genes, and 22 transfer RNAs, with a GC ratio of 25.2%. In total, 353 SNPs and 11 INDEL regions (total length 67 bp) were found against the previously sequenced M. differentialis mitochondrial genome recorded as public genome data. The number of interspecific variations was greater than the number of intraspecific variations in this insect. Phylogenetic tree analysis showed that the mitochondrial genome clustered the Melanoplus clade with two previously reported Melanoplus sequences. However, the sequences were not divided at the species‐level clade possibly as a consequence of misidentification caused by an error in the public database. Our results extend the molecular database status of Melanoplus by providing a novel complete mitochondrial genome sequence for M. differentialis that could serve as reference for further molecular studies.

Daphne pseudomezereum A. Gray var. koreana (Nakai) Hamaya is a shrub distributed in high mountains in Japan and Korea and is used as a medicinal plant. The complete chloroplast genome of D. pseudomezereum var. koreana is 171,152 bp long with four subregions consisting of a large single-copy region (84,963 bp), a small single-copy region (41,725 bp), and a pair of inverted repeats (2739 bp). The genome includes 139 genes (93 protein-coding genes, eight rRNAs, and 38 tRNAs). Phylogenetic analyses show that D. pseudomezereum var. koreana is nested within the Daphne clade in the narrow sense and that it forms a distinct lineage.

2'-O-methylation (2OM) is the most common post-transcriptional modification of RNA. It plays a crucial role in RNA splicing, RNA stability and innate immunity. Despite advances in high-throughput detection, the chemical stability of 2OM makes it difficult to detect and map in messenger RNA. Therefore, bioinformatics tools have been developed using machine learning (ML) algorithms to identify 2OM sites. These tools have made significant progress, but their performances remain unsatisfactory and need further improvement. In this study, we introduced H2Opred, a novel hybrid deep learning (HDL) model for accurately identifying 2OM sites in human RNA. Notably, this is the first application of HDL in developing four nucleotide-specific models [adenine (A2OM), cytosine (C2OM), guanine (G2OM) and uracil (U2OM)] as well as a generic model (N2OM). H2Opred incorporated both stacked 1D convolutional neural network (1D-CNN) blocks and stacked attention-based bidirectional gated recurrent unit (Bi-GRU-Att) blocks. 1D-CNN blocks learned effective feature representations from 14 conventional descriptors, while Bi-GRU-Att blocks learned feature representations from five natural language processing-based embeddings extracted from RNA sequences. H2Opred integrated these feature representations to make the final prediction. Rigorous cross-validation analysis demonstrated that H2Opred consistently outperforms conventional ML-based single-feature models on five different datasets. Moreover, the generic model of H2Opred demonstrated a remarkable performance on both training and testing datasets, significantly outperforming the existing predictor and other four nucleotide-specific H2Opred models. To enhance accessibility and usability, we have deployed a user-friendly web server for H2Opred, accessible at https://balalab-skku.org/H2Opred/. This platform will serve as an invaluable tool for accurately predicting 2OM sites within human RNA, thereby facilitating broader applications in relevant research endeavors.

Owing to the rapid development of sequencing technologies, more than 1,000 plant genomes have been sequenced and released. Among them, 69 Korean plant taxa (85 genome sequences) contain at least one whole-genome sequence despite the fact that some samples were not collected in Korea. The sequencing-by-synthesis method (next-generation sequencing) and the PacBio (third-generation sequencing) method were the most commonly used in studies appearing in 65 publications. Several scaffolding methods, such as the Hi-C and 10x types, have also been used for pseudo-chromosomal assembly. The most abundant families among the 69 taxa are Rosaceae (10 taxa), Brassicaceae (7 taxa), Fabaceae (7 taxa), and Poaceae (7 taxa). Due to the rapid release of plant genomes, it is necessary to assemble the current understanding of Korean plant species not only to understand their whole genomes as our own plant resources but also to establish new tools for utilizing plant resources efficiently with various analysis pipelines, including AI-based engines.

Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum , a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects. Keywords , , mitochondrial genome , truffle , NGS reads , intraspecific variations , simple sequence repeats , phylogenetic analysis , Coleoptera , Bostrichoidea , Ptinidae

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.

Atriplex gmelinii C. A. Mey. Ex Bong._1838 is an annual halophytic herb found in East Asia and North America. The chloroplast genome of A. gmelinii was successfully sequenced. The assembled genome (151,852 bp; GC ratio, 37.3%) is composed of four subregions, with the large single copy (LSC; 83,872 bp; 35.4%) and small single copy (SSC; 17,812 bp; 30.9%) regions separated by two regions of inverted repeat regions (25,084 bp; 42.8%). A total of 130 genes were predicted with 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. The phylogenetic analyses inferred from whole chloroplast genomes of 35 species, including 34 species in Amaranthaceae and one outgroup species, suggest a close relationship between A. gmelinii and A. centralasiatica.

We sequenced the complete mitochondrial genome of Aclees taiwanensis collected in Korea. The circular mitogenome of A. taiwanensis is 17,435 bp, longer than that of Aclees cribratus, and includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a control region/D-loop. The AT ratio is 75.4%. Maximum-likelihood and Bayesian inference phylogenetic trees showed that A. taiwanensis was clustered with A. cribratus with full-support values for both trees.

We have determined the complete chloroplast genome of Chrysanthemum zawadskii Herbich isolated in Korea. The circular chloroplast genome of C. zawadskii is 151,137 bp long and has four subregions: 83,041 bp of large single copy and 18,350 bp of small single copy regions are separated by 24,873 bp of inverted repeat regions including 133 genes (87 protein-coding genes, eight rRNA genes, 37 tRNAs, and one pseudogene). There are 65 to 152 single nucleotide polymorphisms and 33 to 64 insertion and deletion regions (178 bp to 372 bp in length) identified against three available chloroplast genomes of C. zawadskii. The phylogenetic tree shows that C. zawadskii is clustered as a paraphyletic group with C. zawadskii subsp. coreanum, displaying incongruency between species and clades.

Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.

Diarthron linifolium Turcz. is an annual herb usually found in sandy soil or limestone areas. Plants in the genus Diarthron are known to have toxic chemicals that may, however, be potentially useful as an anticancer treatment. Diarthron linifolium is a unique species among the species of the genus distributed in Korea. Here, we determine the genetic variation of D. linifolium collected in Korea with a full chloroplast genome and investigate its evolutionary status by means of a phylogenetic analysis. The chloroplast genome of Korean D. linifolium has a total length of 172,644 bp with four subregions; 86,158 bp of large single copy and 2,858 bp of small single copy (SSC) regions are separated by 41,814 bp of inverted repeat (IR) regions. We found that the SSC region of D. linifolium is considerably short but that IRs are relatively long in comparison with other chloroplast genomes. Various simple sequence repeats were identified, and our nucleotide diversity analysis suggested potential marker regions near ndhF. The phylogenetic analysis indicated that D. linifolium from Korea is a sister to the group of Daphne species.