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Utricularia tenuicaulis Miki 1935 is an aquatic carnivorous plant species found in East Asia including Korea and Japan. In this study, the chloroplast genome of U. tenuicaulis was successfully sequenced. The assembled genome (153,976 bp; GC ratio, 37.0%) contains four subregions, with the large single copy (LSC; 84,596 bp; 34.9%) and small single copy (SSC; 17,946 bp; 30.5%) regions separated by 25,718 bp of inverted repeat regions (42.7%), and includes 126 genes (81 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses based on the whole-chloroplast genomes of 18 species, including 17 Lentibulariaceae species and one outgroup species, suggest a close relationship between U. tenuicaulis and Utricularia macrorhiza Leconte 1824. A comparison of genomic variation between U. tenuicaulis and U. macrorhiza confirmed the validity of the specific discrimination of U. tenuicaulis. [ABSTRACT FROM AUTHOR]

Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates. [ABSTRACT FROM AUTHOR]

We presented a complete chloroplast genome of a new species candidate of Plantago depressa, Willd. named as Plantago wonjuenesis sp. nov, which is 164,946 bp long (GC ratio is 38.0%) and has four subregions: 82,985 bp of large single copy and 4,647 bp of small single-copy regions are separated by 38,657 bp of inverted repeat regions including 94 protein-coding genes (PCGs), eight rRNAs, and 38 tRNAs. Number of variations between P. wonjuenesis and P. depressa can be considered as interspecific variations. Bootstrapped phylogenetic trees constructed with conserved 78 PCGs of eleven Plantaginaceae chloroplast genomes present that P. wonjuensis is clustered with P. depressa, P. fengdouensis, and P. media. [ABSTRACT FROM AUTHOR]

We de novo assembled the complete mitochondrial genome of the green peach aphid, Myzus persicae, using its genomic DNA isolated from the bell pepper in Korea. The circular mitogenome of M. persicae is 16,936 bp long and contains the standard 37 genes: 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as a single control region of 798 bp. Given the high AT ratio (84.1%) of the M. persicae mitogenome, we found, through the comparison of the Chinese M. persicae mitogenomes, that approximately 1.6% of the mitogenome is polymorphic, including 30 single nucleotide polymorphisms (SNPs), 12 insertions and deletions (INDELs), and large sequence variations in the control region. To resolve the phylogenetic position of M. persicae, we analyzed all mitochondrial protein-coding genes from 38 species within the Aphidoidea superfamily, with Adelges laricis as an outgroup. Our M. persicae sample was significantly grouped with three existing M. persicae samples, and the species belonging to the family Aphididae formed a monophyletic clade. [ABSTRACT FROM AUTHOR]

We have determined the second mitochondrial genome of Epanerchodus koreanus Verhoeff, 1937 collected in limestone cave of Korea. The circular mitochondrial genome of E. koreanus is 15,581 bp long. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was different from the rest three Polydesmida mitochondrial genomes, resulted from relocation of tRNAs, rRNAs, and ND1. The base composition was AT-biased (75.1%). Phylogenetic trees displayed phylogenetic relationship, which is congruent to previous study, except Sphaerotheriidae sp. clustering with Helminthomorpha. [ABSTRACT FROM AUTHOR]

Rhopalosiphum nymphaeae (Linnaeus, 1761) is a heteroecious polyphagous aphid, which can survive underwater. We have determined mitochondrial genome of R. nymphaeae collected in Korea. The circular mitogenome of R. nymphaeae is 15,594 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 874 bp. The base composition was AT-biased (84.3%). Phylogenetic trees present that genus Rhopalosiphum is polyphyletic, requiring more investigation of mitochondrial genomes. [ABSTRACT FROM AUTHOR]

Hipparchia autonoe (Esper, 1783) is a protected butterfly species found in Mt. Halla in South Korea. We have determined mitochondrial genome of H. autonoe collected in Mt. Halla. The circular mitogenome of H. autonoe is 15,300 bp long, which is shorter than previously sequenced mitogenome by 189 bp due to differences of tandem repeats. It includes 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNAs. The base composition was AT-biased (78.9%). Nineteen single nucleotide polymorphisms and one insertion and deletion were identified between the two individuals of H. autonoe captured in Mt. Halla, presenting enough genetic diversity of H. autonoe within population. [ABSTRACT FROM AUTHOR]

Rotunda rotundapex (Miyata & Kishida, 1990) is a silk moth identified in Korea. We completed its mitochondrial genome which is 15,298 bp long and the shortest mitogenome of Bombycidae s.str. It includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. Comparison with COI sequence of Taiwan isolate suggests the Korean population of this species can be a novel species. Gene order of R. rotundapex mitogenome is conserved as in other Bombycidae species. Phylogenetic trees show that R. rotundapex is closely related to genus Rondotia. [ABSTRACT FROM AUTHOR]

Aphaenogaster famelica (Smith, 1874) is a slender ant found in Korea. We have completed the mitochondrial genome of A. famelica of which length is 19,464 bp, the third longest ant mitogenome so far. It was AT-biased (GC ratio is 18.0%) and includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The extra bases of A. famelica are placed in intergenic regions each between trnV-trnM and trnI-trnQ. Gene order of A. famelica is identical to other Myrmicinae ants. Phylogenetic trees show that tribe Stenammini and tribe Myrmicini are closely related. [ABSTRACT FROM AUTHOR]

The fall armyworm, Spodoptera frugiperda, is a serious pest in large numbers on more than 350 plant species in the world. We have determined a 15,388 bp mitogenome of S. frugiperda which includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. The base composition was AT-biased (81.3%). Phylogenetic trees present that Korean S. frugiperda placed in basal position of S. frugiperda clade. S. frugiperda mitochondrial genome can be used for understanding recent active migration of S. frugiperda. [ABSTRACT FROM AUTHOR]

Chloroplast genome of Sang Jae, new candidate cultivar of Abeliophyllum distichum Nakai, has been sequenced to reveal infraspecific relationship of wildtypes and cultivars. Its length is 156,008 bp long (GC ratio is 37.8%) and has four subregions: 86,773 bp of large single copy (35.8%) and 17,827 bp of small single copy (31.9%) regions are separated by 25,704 bp of inverted repeat (43.2%) regions including 133 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic trees show that A. distichum is clustered with twelve Forsythia species and intraspecies variations level is similar to Olea europaea. [ABSTRACT FROM AUTHOR]

Aconitum coreanum (H. Lév.) Rapaics listed in the Korean Red List is a medicinal herb. We presented complete chloroplast genome, which is 157,024 bp long and has four subregions: 87,637 bp of large single-copy and 16,901 bp of small single-copy regions, which are separated by two 26,243 bp inverted repeat regions including 132 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast is 38.0%. Phylogenetic trees show that A. coreanum occupied a basal position at subgenus Aconitum clade and two A. coreanum isolated from midwestern and eastern regions of Korea are clustered together. [ABSTRACT FROM AUTHOR]

Aphid gosypii Glover, 1877 is a widely recognized economically important aphid species in the world. We have determined mitochondrial genome of A. gossypii collected in Korean peninsula. The circular mitogenome of A. gossypii is 15,872 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single control region of 627 bp. The base composition was AT-biased (83.8%). In comparison of Chinese A. gossypii mitochondrial genomes with that of Korean sample, 61 single nucleotide polymorphisms and 3 insertions and deletions were identified, presenting lower level of those of Nilaparvata lugens, Laodelphax striatellus, and Chilo suppresallis. [ABSTRACT FROM AUTHOR]

Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989 bp long and has four subregions: 86,227 bp of large single copy (LSC) and 18,816 bp of small single copy (SSC) regions are separated by 25,793 bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations. [ABSTRACT FROM AUTHOR]

Neocaridina heteropoda koreana Kubo, 1938 is a freshwater shrimp native to the Korean peninsula. We have determined the mitogenome of N. heteropoda koreana, which's length is 15,558 bp long including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 674 bp. Its GC ratio is 33.0%. Gene order of N. heteropoda koreana is identical to those of other known Atyidae species. Phylogenetic trees show that N. heteropoda koreana is sister to N. davidi and placed within genus Caridina. Our mitogenome will be a useful resource for understanding molecular phylogeny of genus Neocradina. [ABSTRACT FROM AUTHOR]

Abeliophyllum distichum Nakai is the only species in Abeliophyllum genus, which is Korean endemic. Ok Hwang 1ho, the first official cultivar of A. distichum., displays that colour of corolla is light yellow (8D and 9D). Here, we completed chloroplast genome of A. distichum cultivar Ok Hwang 1ho to understand genetic diversity of A. distichum cultivar. Its length is 156,008 bp long and has four subregions: 86,773 bp of large single copy (LSC) and 17,827 bp of small single copy (SSC) regions are separated by 25,704 bp of inverted repeat (IR) regions including 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC contents of this chloroplast genome are 37.8% and in the LSC, SSC, and IR regions are 35.8%, 31.9%, and 43.2%, respectively. Ninety-three single nucleotide polymorphisms (SNPs) and 56 insertion and deletions (INDELs) are identified against previous A. distichum chloroplast genome. Phylogenetic trees show that A. distichum is clustered with two Forsythia species and many cultivars of Olea europaea subspecies present shorter branches than that of A. distichum. Our chloroplast genome will be a fundamental data to understand morphological diversity of A. distuichum. [ABSTRACT FROM AUTHOR]

As a Korean endemic plant, Salix koriyanagi Kimura ex Goerz belongs to the genus Salix L. which is the largest genus of Salicaceae. In this study, we presented a complete chloroplast genome from male individual of S. koriyanagi which is 155,548 bp and has four subregions: 84,415 bp of large single copy (LSC) and 16,125 bp of small single copy (SSC) regions are separated by 27,459 bp of inverted repeat (IR) regions including 131 genes (85 protein-coding gene, 8 rRNAs, and 38 tRNAs). The overall GC content of the chloroplast genome is 36.7% and those in the LSC, SSC, and IR regions are 34.4%, 31.0%, and 41.9%, respectively. SSC is inverted in comparison to that of female individual of S. koriyanagi. Phylogenetic trees show phylogenetic relationship of Salix and Populus genera. [ABSTRACT FROM AUTHOR]

Camellia japonica L. is an ornamental species due to its beautiful red flowers blooming in winter. Here, we completed the chloroplast genome of C. japonica isolated in Soyeonpyeongdo located at the northernmost in South Korea. Its length is 156,971 bp long and has four subregions: 86,673 bp of a large single copy (LSC) and 18,394 bp of small single copy (SSC) regions are separated by 25,952 bp of inverted repeat (IR) regions including 135 genes (91 protein-coding genes, 8 rRNAs, and 36 tRNAs). The overall GC content of this chloroplast genome is 37.3% and those in the LSC, SSC, and IR regions are 35.3%, 30.5%, and 43.0%, respectively. Twenty-five single nucleotide polymorphisms (SNPs) and two insertions and deletions (INDELs) are identified against Korean C. japonica isolated in Jeju island, while 78 SNPs and 643 INDELs are found against Chinese C. japonica. Phylogenetic trees show that Camellia chekiangoleosa is clustered with Korean C. japonica. [ABSTRACT FROM AUTHOR]

Simple Summary: We completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH. [ABSTRACT FROM AUTHOR]

Nylanderia flavipes (Smith, 1874) is a Formicine ant found in East Asia. We have completed mitochondrial genome of N. flavipes of which length is 16,687 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. The base composition was AT-biased (GC ratio is 18.9%). Gene order of N. flavipes presents a unique inversion of trnP in comparison to Camponotus species. Our phylogenetic trees together with phylogenomic analysis suggest that the gene order rearrangements occurred independently in Camponotus and N. flavipes. [ABSTRACT FROM AUTHOR]

Cirsium rhinoceros (H.Lév. & Vaniot) Nakai has been used a traditional medicine. Complete chloroplast genome of C. rhinoceros is 152,576 bp long and has four subregions: 87,262 bp of large single copy (LSC) and 21,486 bp of small single copy (SSC) regions that are separated by 18,742 bp of inverted repeat (IR) regions including 133 genes (88 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.7% and in the LSC, SSC, and IR regions are 36.0%, 31.4%, and 43.8%, respectively. Phylogenetic trees show that Cirsium species are clustered along with their distribution. [ABSTRACT FROM AUTHOR]

Populus alba x Populus glandulosa is a hybrid species made by Dr. Hyun. It is called as Hyunsasi tree in Korea. It has been used as a good resource for genetic engineering because it is sterile. Here, we presented its complete chloroplast and mitochondrial genomes: chloroplast genome is identical to that of P. alba (156,505 bp and 129 genes covering 84 protein-coding genes, 37 tRNAs, and eight rRNAs) and mitochondrial genome is 813,261 bp long and GC ratio is 44.9%. It contains 59 genes containing 32 protein-coding genes, 22 tRNAs, and three rRNAs. Based on alignment with P. tremula x P. alba mitochondrial genome, 1,752 single nucleotide polymorphisms (SNPs; 0.22%) and 41,506 insertion and deletions (INDELs; 5.10%) are found. Phylogenetic trees based on chloroplast and mitochondrial genomes show different topology in four Populus species, indicating that both genomes may be evolved in different ways after common ancestors of Populus genus. [ABSTRACT FROM AUTHOR]

Ilex integra Thunb. is an ornamental tree distributed in Korea, Taiwan, mid-Southern China, and Japan. To understand the genetic differences between I. integra and I. cornuta, we presented complete chloroplast genome of I. integra, which is 157,548 bp long and has four subregions: 86,935 bp of large single copy (LSC) and 18,426 bp of small single copy (SSC) regions are separated by 26,093 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.6% and those in the LSC, SSC, and IR regions are 35.7%, 31.9%, and 42.9%, respectively. Phylogenetic trees show that I. integra is clustered with I. cornuta and I. latifolia. Sequence variations identified from I. integra and I. corunta presents that both species have enough sequence variations as different species. [ABSTRACT FROM AUTHOR]

Camellia japonica L. usually blooms red flower in winter in Jeju island, Korea, considered a species which should not be planted in the garden. Here, we completed chloroplast genome of C. japonica isolated in Seogwang-ri, Jeju island for comparing that isolated in Wimi-ri, Jeju island. Its length is 156,971 bp long and has four subregions: 86,673 bp of large single copy (LSC) and 18,394 bp of small single copy (SSC) regions are separated by 25,952 bp of inverted repeat (IR) regions including 135 genes (91 protein-coding genes, eight rRNAs, and 36 tRNAs). Its overall GC content is 37.3% and those in the LSC, SSC, and IR regions are 35.3%, 30.5%, and 43.0%, respectively. One insertion and one deletion are identified between chloroplast genomes of Soyeonpyeong island and Seogwang-ri, even though both places are far enough (>450 km). Twenty-five single nucleotide polymorphisms (SNPs) are identified within two Jeju island chloroplast genomes, presenting that C. japonica tree in Wimi-ri is genetically far from the two chloroplast genomes. Trees also show that genetic diversity of C. japonica is lower than that of C. sinensis. [ABSTRACT FROM AUTHOR]

Coffea arabica is major cultivated species of coffee. We selected cold hardiness of C. arabica (named as CH3) based on selection of coffee seeds in Jeju Island, Korea. Here, we presented complete chloroplast genome of cold resistance C. arabica which is 155,192 bp long and has four subregions: 85,163 bp of large single copy (LSC) and 18,137 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.3%, 31.3%, and 43.0%, respectively. Three non-synonymous single nucleotide polymorphisms and three insertions and deletions are found, indicating that further analysis will be required to understand genetic elements of cold hardiness of CH3. [ABSTRACT FROM AUTHOR]

Illicium anisatum L. is a neighbor species of Illicium verum used for making anti-virus vaccine. Here, we completed the chloroplast genome of I. anisatum. Its length is 142,747 bp long and has four subregions: 100,833 bp of large single copy (LSC) and 20,227 bp of small single copy (SSC) regions are separated by 10,844 bp of inverted repeat (IR) including 123 genes (81 protein-coding genes, 8 rRNAs, and 34 tRNAs). The overall GC content of this chloroplast genome is 39.2% and those in the LSC, SSC, and IR regions are 38.1%, 33.9%, and 49.3%, respectively. Twenty-one single nucleotide polymorphisms (SNPs) and 114 insertion and deletions (INDELs) are identified against I. anisatum originated from Green Farmacy Garden. Interestingly, 12 INDEL clusters, of which length ranges from 2 bp to 21 bp are identified, which is like the case of Duchesnea chrysantha. Phylogenetic trees show that five Illicium chloroplast genomes form Illicium clade, clearly. [ABSTRACT FROM AUTHOR]

Rhynchocypris oxycephalus (Sauvage and Dabry de Thiersant, 1874) distributed in East Asia is small cold-water fish. We completed whole mitochondrial genome of R. oxycephalus caught in Korea. Its length is 16,583 bp, which is shorter than those of three mitochondrial genomes from China and Japan. Three hundred ninety seven of 1,278 SNPs and 27 of 44 INDELs are Korean R. oxycephalus specific. It contains 13 protein-coding genes, 2 rRNAs and 22 tRNAs and its GC ratio is 44.5%. Phylogenetic analysis presents genetic diversity of R. oxycephalus originated from Korea, Japan, and China. [ABSTRACT FROM AUTHOR]

We have determined the mitochondrial genome of Chilo suppressalis (Walker, 1863) collected in Korea. The circular mitogenome of C. suppressalis was 15,341 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 622 bp. The base composition was AT-biased (93.6%). Through alignment of three C. suppresalis mitochondrial genomes, 79 single nucleotide polymorphisms (8.8%) and 291 insertions and deletions (33.3%) are identified as Korean C. suppressalis specific variations. Phylogenetic trees present that three mitochondrial genomes of C. suppressalis have enough variations within a species, which can be a candidate to understand its origin and geographical distribution using molecular marker sequences. [ABSTRACT FROM AUTHOR]

To study the intraspecific variation of the sea cucumber, Apostichopus japonicus, we sequenced three complete mitochondrial genomes, especially from different body color variants (green, black, and red) of Apostichopus japonicus in Geomum-do, Republic of Korea. The full lengths of green, black, and red sea cucumber mitochondrial genomes are 16,106 bp, 16,096 bp, and 16,107 bp, respectively. They all contain 37 genes (13 protein-coding genes, 2 rRNAs, and 22 tRNAs), and have an average 38.0% of GC ratio. Two hundred thirty eight single nucleotide polymorphisms and 26 insertion and deletions were identified among three sea cucumber mitochondrial genomes. The phylogenetic analysis of A. japonicus with additional 14 available A. japonicus and two Parastichopus mitochondrial genomes were used as outgroups shows somewhat distinct three clades with body color patterns. Furthermore, there is no clear phylogenetic separation among Korean, Chinese, and Japanese individuals. These data will provide new insights and to facilitate the rapid growth of the sea cucumber aquaculture industry and its breeding programs. [ABSTRACT FROM AUTHOR]