Geographic Genetic Contour of a Ground Beetle, Scarites aterrimus (Coleoptera: Carabidae) on the Basis of Mitochondrial DNA Sequence

( Ah Rha Wang ),( Min Jee Kim ),( Young Bok Cho ),( Xin Long Wan ),( Ik Soo Kim ) 한국잠사학회 2011 International Journal of Industrial Entomology Vol.22 No.2

The Scarites aterrimus (Coleoptera: Carabidae), is one of the carabid beetles dwelling exclusively on coastal sandy dunes. Habitat deterioration and equivalent activity have greatly concerned population declines in several species dwelling on the coastal sandy dunes. As a first step to establish long-term conservation strategy, we investigated the nation-wide magnitude and nature of genetic diversity of the species. As a first step, we sequenced a portion of mitochondrial COI gene, corresponding to "DNA Barcode" region (658 bp) from a total of 24 S. aterrimus individuals collected over nine sandy dunes belonging to four Korean provinces. The sequence analysis evidenced moderate to low magnitude of sequence diversity compared with other insect species distributed in Korean peninsula (0.152% to 0.912%). The presence of closely related haplotypes and relatively high gene flow estimate collectively suggest that there had been no historical barriers that bolster genetic subdivision. Population decline was postulated on the basis of several missing haplotypes that are well found in the species with a large population size. This interpretation is consistent with field observation of small population size in the coastal sandy dune habitats. The highest genetic diversity estimates were found in the coastal sand dune population of Seogwipo, Jeju Island, justifying a prior attention to the population, in order to sustain overall genetic diversity of the species. Further scrutinized study might be required for further robust conclusion.

Phylogeny of Apis with the description of newly sequenced mitochondrial genomes of Apis species (Hymenoptera: Apidae)

Ah Rha Wang,Jong Seok Kim,Min Jee Kim,Hye-Kyung Kim,Yong Soo Choi,Iksoo Kim 한국응용곤충학회 2016 한국응용곤충학회 학술대회논문집 Vol.2016 No.04

We sequenced complete mitochondrial genomes (mt genomes) of four Apis species, such as A. cerana, A. dorsata, A. laboriosa, and A. mellifera ligustica. The A. m. ligustica used in this study was originated from United States and selected for a high hygienic behavior during several years of breeding program. Considering current phylogenetic hypothesis of Apis the positive relationships between phylogeny and gene rearrangement was not supported. Phylogenetic reconstruction using available Apoidea species has shown the relationships ((Apidae + Colletidae) + Crabronidae). Within Apis, a strong support for three groups was obtained: A. florea and A. andreniformis as a basal group to the other A. cerana and A. mellifera group and A. dorsata and A. laboriosa group. The test to find out suitable single mt gene for the phylogeny at the genus level and below-genus level of Apis provided an identical topology from ND4L and ND6 in the ML analysis and ND3 and NF4L in the BI analysis to that from whole mt genome, with relatively strong support, indicating that these individual genes can potentially be utilized for within-species level phylogeny of Apis.

Single Nucleotide Polymorphisms from Mitochondrial Genomes that Diagnose the Honey Bee Strains (Apis mellifera ligustica) with the High and Low Hygienic Behaviors

Ah Rha Wang,Jong Seok Kim,Min Jee Kim,Keon Hee Lee,Iksoo Kim 한국응용곤충학회 2018 한국응용곤충학회 학술대회논문집 Vol.2018 No.04

The honey bee, Apis mellifera ligustica (Hymenoptera: Apidae), strain with a high hygienic behavior (HHB) has been bred for several years in Korea, and a diagnosis system to distinguish it from low hygienic behavior (LHB) strain has been necessitated. Thus, complete mitogenome of the two strains were sequenced through Next-Generation Sequencing technique to detect SNPs. Comparison of the mitogenome sequences from the two strains of A. m. ligustica have detected 23 SNPs in 11 PCGs and these were further confirmed the presence of SNPs using each 10 individuals selected randomly from each strain, indicating that these SNP markers might be useful to diagnose the honeybee strains with the HHB. Therefore, mitogenome sequences are promising genome source to detect SNP markers, particularly for inbred female iso-lines.

Geographic Genetic Contour of a Ground Beetle, Scarites aterrimus (Coleoptera: Carabidae) on the Basis of Mitochondrial DNA Sequence

Wang, Ah-Rha,Kim, Min-Jee,Cho, Young-Bok,Wan, Xinlong,Kim, Ik-Soo Korean Society of Sericultural Science 2011 International Journal of Industrial Entomology Vol.22 No.2

The Scarites aterrimus (Coleoptera: Carabidae), is one of the carabid beetles dwelling exclusively on coastal sandy dunes. Habitat deterioration and equivalent activity have greatly concerned population declines in several species dwelling on the coastal sandy dunes. As a first step to establish long-term conservation strategy, we investigated the nation-wide magnitude and nature of genetic diversity of the species. As a first step, we sequenced a portion of mitochondrial COI gene, corresponding to "DNA Barcode" region (658 bp) from a total of 24 S. aterrimus individuals collected over nine sandy dunes belonging to four Korean provinces. The sequence analysis evidenced moderate to low magnitude of sequence diversity compared with other insect species distributed in Korean peninsula (0.152% to 0.912%). The presence of closely related haplotypes and relatively high gene flow estimate collectively suggest that there had been no historical barriers that bolster genetic subdivision. Population decline was postulated on the basis of several missing haplotypes that are well found in the species with a large population size. This interpretation is consistent with field observation of small population size in the coastal sandy dune habitats. The highest genetic diversity estimates were found in the coastal sand dune population of Seogwipo, Jeju Island, justifying a prior attention to the population, in order to sustain overall genetic diversity of the species. Further scrutinized study might be required for further robust conclusion.

Geographic Genetic Contour of a Ground Beetle, Scarites aterrimus (Coleoptera: Carabidae) on the Basis of Mitochondrial DNA Sequence

Ah Rha Wang,Min Jee Kim,Young Bok Cho,Xinlong Wan,Iksoo Kim 한국응용곤충학회 2011 한국응용곤충학회 학술대회논문집 Vol.2011 No.05

The Scarites aterrimus (Coleoptera: Carabidae), is one of the carabid beetles dwelling exclusively on coastal sandy dunes. Recent habitat deterioration has greatly concerned population declines in several species dwelling on the coastal sandy dunes. Asa first step to establish long-term conservation strategy, we investigated the nation-wide magnitude and nature of genetic diversity of the species. As a first step, we sequenced a portion of mitochondrial COI gene, corresponding to “DNA Barcode” region (658 bp) from a total of 24 S. aterrimus individuals collected over nine sandy dunes belonging to four Korean provinces. The sequence analysis evidenced moderate to low magnitude of sequence diversity compared with other insect species distributed in Korean peninsula (0.152% to 0.912%). The presence of closely related haplotypes and relatively high gene flow estimate collectively suggest that there had been no historical barriers that bolster genetic subdivision. Population decline was postulated on the basis of several missing haplotypes that are well found in the species with a large population size. This interpretation is consistent with field observation of small population size in the coastal sandy dune habitats. The highest genetic diversity estimates were found in the coastal sand dune population of Seogwipo, Jeju Island, justifying a prior attention to the population, in order to sustain overall genetic diversity of the species. Further scrutinized study might be required for further robust conclusion.

Complete Mitochondrial Genome of the Burmese giant Earthworm, Tonoscolex birmanicus (Clitellata: Megascolecidae)

Ah Rha Wang,Yong Hong,Tin Moe Win,Iksoo Kim 한국응용곤충학회 2013 한국응용곤충학회 학술대회논문집 Vol.2013 No.10

Up to now the complete mitochondrial genome (mitogenome) sequences of only three species of clitellate have been available. We have determined the complete mitogenome sequences of the elusive Burmese giant earthworm Tonoscolex birmanicus (Clitellata: Megascolecidae), which is endemic to Myanmar. The 15,170-bp long genome contains the 37 genes typical of metazoan mitogenomes [13 protein-coding genes (PCG), two rRNA genes and 22 tRNA genes] and one major non-coding region. All of the 37 genes are transcribed from the same DNA strand. The arrangement of the T. birmanicus mitogenome is identical to that of two within-ordinal species Lumbricus terrestris and Perionyx excavates. All 13 PCGs start with the ATG. For the stop codon, only six PCGs end with the TAA, whereas the remaining ones ends with the incomplete stop codon, T. Genes overlap in a total of 14 bp in five locations, and harbor a total of 16 bp of intergenic spacer sequences in nine locations.

The Complete Mitochondrial Genome of Erynnis montanus (Lepidoptera: Hesperiidae):A New Gene Arrangement in Lepidoptera

Ah Rha Wang,Heon Cheon Jeong,Yeon Soo Han,Iksoo Kim 한국응용곤충학회 2013 한국응용곤충학회 학술대회논문집 Vol.2013 No.04

Gene arrangement in the mitochondrial genome (mitogenome) has been regarded as an important evolutionary event that is useful as a phylogenetic signal. The mountainous duskywing, Erynnis montanus, belongs to a lepidopteran family Hesperiidae. We sequenced 15,530-bp long complete mitogenome of the species. The genome has the typical gene content of animals (13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one major non-coding A+T-rich region). Further, E. montanus mitogenome also contained a high A/T content in the whole genome (81.7%) and the CGA (arginine) as the start codon for the COI gene, as typical in lepidopteran mitogenome. However, unlike other lepidopteran species, including two sequenced skippers, the E. montanus mitogenome has a unique arrangement tRNASer-tRNAAsn, instead of the tRNAAsn-tRNASer found unanimously in other lepidopteran species, providing a new gene arrangement in Lepidoptera. Such rearrangement probably was likely caused by duplication of gene block tRNASer-tRNAAsn and subsequent random loss of tRNAAsn in the first copy and tRNASer in the second copy, resulting in the arrangement tRNASer-tRNAAsn. Considering current phylogenetic relationships among available lepidopteran groups in connection with lepidopteran gene arrangement the new gene arrangement found in E. montanus seems to be apomorphy, requiring cautious interpretation as a phylogenetic signal.

The mitochondrial genome of the black dwarf honey bee, Apis andreniformis (Hymenoptera: Apidae)

Ah Rha Wang,Min Jee Kim,Joo Young Lee,Yong Soo Choi,Ratna Thapa,Iksoo Kim 한국양봉학회 2014 한국양봉학회 학술대회 자료집 Vol.2014 No.9

The complete mitochondrial genome of the mountainous duskywing, <i>Erynnis montanus</i> (Lepidoptera: Hesperiidae): a new gene arrangement in Lepidoptera

Wang, Ah Rha,Jeong, Heon Cheon,Han, Yeon Soo,Kim, Iksoo Informa UK Ltd. 2014 Mitochondrial DNA Vol.25 No.2

<P>The mountainous duskywing, <I>Erynnis montanus</I>, belongs to a lepidopteran family Hesperiidae. The 15,530-bp long complete mitochondrial genome (mitogenome) of the species has the typical gene content of animals (13 protein-coding genes, two rRNA genes, 22 tRNA genes and one major non-coding <I>A</I>+<I>T</I>-rich region). As typical in lepidopteran mitogenome <I>E. montanus</I> mitogenome also contained a high <I>A</I>/<I>T</I> content in the whole genome (81.7%) and the CGA (arginine) as the start codon for the COI gene. Unlike other lepidopteran species, including two sequenced skippers, the <I>E. montanus</I> mitogenome has a unique arrangement tRNA<SUP>Ser</SUP>-tRNA<SUP>Asn</SUP>, instead of the tRNA<SUP>Asn</SUP>-tRNA<SUP>Ser</SUP> found unanimously in other lepidopteran species, providing a new gene arrangement in Lepidoptera. Such rearrangement probably was likely caused by duplication of gene block tRNA<SUP>Ser</SUP>-tRNA<SUP>Asn</SUP> and subsequent random loss of tRNA<SUP>Asn</SUP> in the first copy and tRNA<SUP>Ser</SUP> in the second copy, resulting in the arrangement tRNA<SUP>Ser</SUP>-tRNA<SUP>Asn</SUP>.</P>

Complete mitochondrial genome of the dwarf honeybee, <i>Apis florea</i> (Hymenoptera: Apidae)

Wang, Ah Rha,Kim, Min Jee,Park, Jeong Sun,Choi, Yong Soo,Thapa, Ratna,Lee, Kwang Youll,Kim, Iksoo Informa Healthcare 2013 Mitochondrial DNA Vol.24 No.3

<P>In this study, the 17,694-bp long complete mitochondrial genome (mitogenome) of the dwarf honeybee, <I>Apis</I> <I>florea</I> (Hymenoptera: Apidae), was described, and a noteworthy triplicated tRNA<SUP>ser</SUP>(AGN) region and an extraordinary long A+T-rich region with repeat regions were identified. The gene arrangement of <I>A. florea</I> mitogenome was identical to that of <I>Apis mellifera</I>, but it contained three tRNA<SUP>Ser</SUP>(AGN), each of which was preceded by a 44-bp-long repeat unit and followed by a 64-bp-long repeat unit plus one complete first repeat adjacent to tRNA<SUP>Met</SUP>. A total of 1610-bp long two repeat regions in 1987-bp long A+T-rich region were composed of nearly identical 141-219-bp long 5 tandem repeats and 50-52-bp long 12 tandem repeats that were encompassed by three non-repeat sequences. One potential explanation for this repeat sequence is slipped-strand mispairing and unequal crossing-over events during DNA replication.</P>