Ah Rha Wang

Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera

We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A+T composition (79.3%-80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA(Gln) and ND2 (64-87 bp), conserved ATACTAA motif between tRNA(Ser (UCN)) and ND1, and characteristic features of the A+T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA(Asn)/tRNA(Ser (AGN)), instead of the rearrangement tRNA(Ser (AGN))/tRNA(Asn), found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea+Noctuoidea+Geometroidea)+Pyraloidea)+Papilionoidea)+Tortricoidea)+Yponomeutoidea)+Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae+(Hesperiidae+(Pieridae+((Lycaenidae+Riodinidae)+Nymphalidae)))) were strongly supported in all analyses (0.98-1 by BI and 96-100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.

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

Abstract The mountainous duskywing, Erynnis montanus, 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 A+T-rich region). As typical in lepidopteran mitogenome 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. 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.

Complete mitochondrial genome of the dwarf honeybee, Apis florea (Hymenoptera: Apidae)

In this study, the 17,694-bp long complete mitochondrial genome (mitogenome) of the dwarf honeybee, Apis florea (Hymenoptera: Apidae), was described, and a noteworthy triplicated tRNAser(AGN) region and an extraordinary long A+T-rich region with repeat regions were identified. The gene arrangement of A. florea mitogenome was identical to that of Apis mellifera, but it contained three tRNASer(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 tRNAMet. 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.

Complete mitochondrial genome of the Burmese giant earthworm, Tonoscolex birmanicus (Clitellata: Megascolecidae)

Abstract Until 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), 2 rRNA genes and 22 tRNA genes] and 1 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.

Complete mitochondrial genome sequence of the tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae)

The tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae), has been listed as an endangered insect in South Korea. We sequenced the complete 15,112-bp-long mitochondrial genome (mitogenome) of the species. The genome included a typical set of genes (13 protein-coding genes [PCGs], two rRNA genes, and 22 tRNA genes) and one non-coding region with an arrangement identical to that found in most insects. Among the 13 PCGs, only ND1 started with the atypical TTG. The 441-bp-long A+T-rich region possessed the highest A/T content (84.6%) in the genome. N. pygmaea was placed as the sister to Orthetrum species belonging to Libellulidae. Unlike conventional phylogenetic results, the suborders Anisozygoptera and Zygoptera formed a strong sister group in both Bayesian inference (BI) and maximum likelihood (ML) methods (BI, BPP = 1 and ML, 88–94%), justifying the use of different types of molecular markers for phylogenetic analysis.

Mitochondrial DNA variations in Korean Apis cerana (Hymenoptera: Apidae) and development of another potential marker

The geographic relationships and biogeography of Apis cerana have been studied extensively, but Korean populations have not been investigated thoroughly. We sequenced the non-coding region between the tRNALeu and COII mitochondrial (mt) genes (herein named NC2) of Korean samples, along with the samples from seven Asian localities (China, Vietnam, and Thailand). Four undiscovered haplotypes were found in Korea and China, respectively. A phylogenetic analysis confirmed that Korean A. cerana belonged to the Mainland Asian group. Dominance of Japan1 haplotype in Mainland Asia including Korea suggests extensive gene flow and a common genetic origin. A newly developed non-coding region between the tRNAMet and tRNAGln mt genes (named NC1) provided nine haplotypes with twice the number of variable positions compared to those in NC2. A NC1-based phylogenetic analysis revealed the presence of two phylogenetic groups in Apis cerana from Korea suggesting two different sources.

Complete mitochondrial genome of the earthworm, Amynthas jiriensis (Clitellata: Megascolecidae)

Abstract To date, a very limited number of complete clitellate mitochondrial genome (mitogenome) sequences are available. Therefore, in the present study, we elucidated the complete mitogenome sequence of Amynthas jiriensis (Clitellata: Megascolecidae), a species endemic to South Korea. Its 15 151-bp-long genome contains the 37 genes typical of metazoan mitogenomes [13 protein-coding genes (PCG), 2 rRNA genes, and 22 tRNA genes], and one major non-coding control region. All 37 genes were transcribed from the same DNA strand. The arrangement of the A. jiriensis mitogenome is identical to those of all available clitellate mitogenomes. All the 13 PCGs start with the ATG codon. Five PCGs (COI, ND6, CytB, ATP6, and ND4L) end with TAA, and COII ends with TAG, whereas the remaining PCGs end with the incomplete stop codon. The phylogenetic analysis using 13 PCGs has shown the species of Pheretimoid genera, including A. jiriensis, formed a complexity.

Complete mitochondrial genome sequence of Cicindela anchoralis Chevrolat, 1845 (Coleoptera: Carabidae)

Abstract The tiger beetle, Cicindela anchoralis Chevrolat, 1845 (Coleoptera: Carabidae), has been listed as an Endangered insect in South Korea. We sequenced the complete mitochondrial genome (mitogenome) of this organism (16,388 bp). The genome includes a typical set of genes (13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes) and 1 non-coding region with an arrangement identical to that observed in most insect genomes. Twelve PCGs had the typical ATN start codon, whereas ND1 had the atypical TTG codon. The AT-rich region is 1629-bp long, composed of 80.0% A + T nucleotides, and has no long repeat sequences. Phylogenetic analyses with concatenated sequences of the 13 PCGs and 2 rRNA genes, using the Bayesian inference (BI) method, placed C. anchoralis as a sister to the within-subfamilial species Habrodera capensis, with the highest nodal support presented by both BI and maximum likelihood (ML) methods. Three subfamilies represented by more than one species (Cicindelinae, Harpalinae, and Carabinae) were all determined by both BI and ML analyses to form strong monophyletic groups.

Complete mitochondrial genome sequence of Macromia daimoji Okumura, 1949 (Odonata: Macromiidae)

Abstract The dragonfly Macromia daimoji Okumura, 1949 (Odonata: Macromiidae) has been listed as an Endangered insect in South Korea. We sequenced the complete 15,198 bp mitochondrial genome (mitogenome) of this organism, which is the first mitogenome sequence reported from the family Macromiidae. The genome includes a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes) and one non-coding region with an arrangement identical to that observed in most insect genomes. Phylogenetic analyses using concatenated sequences of the 13 PCGs and 2 rRNA genes using the Bayesian inference (BI) method placed Macromiidae, represented by M. daimoji, as a sister group to Libellulidae with the highest nodal support [Bayesian posterior probabilities (BPP) = 1]. Unlike conventional phylogenetic analysis, the suborders Anisozygoptera and Zygoptera formed a strong sister group (BPP =1), justifying the use of different molecular markers for phylogenetic analysis.

Comparative description of mitochondrial genomes of the honey bee Apis (Hymenoptera: Apidae): four new genome sequences and Apis phylogeny using whole genomes and individual genes

We sequenced four complete mitochondrial genomes (mt genomes) of members of the honey bee genus Apis (A. cerana, A. dorsata, A. laboriosa, and A. mellifera ligustica). These four and other available mt genome sequences of Apis were used to scrutinize the within-genus genomic characteristics, gene arrangement, and phylogenetic relationships of Apis. Furthermore, phylogenetic performance of 15 individual genes and two concatenated gene combinations were tested to locate suitable genes for Apis phylogeny. Phylogenetic reconstruction using all concatenated protein-coding genes (PCGs) and rRNAs strongly supported the presence of three lineages in Apis: the sister lineages of cavity-nesting honey bees (A. cerana, A. mellifera, A. nigrocincta, and A. koschevnikovi) and the giant honey bees (A. dorsata and A. laboriosa), and a divergent lineage consisting of the dwarf honey bees (A. florea and A. andreniformis). Apis mt genomes revealed two gene arrangements, trnE–trnS1 or trnS1–trnE in the tRNA block at the A + T-rich region and ND2 junction. The gene arrangement found in Apis are consistent with two independent derivations because the same arrangement was shared between non-sister species. Several number of two gene concatenation, along with the individual gene ND4, confirmed the current whole mt genome-based phylogeny with relatively strong support, signifying that these single and two gene combinations are sufficient for an extended within-genus phylogeny of Apis, without inclusion of additional genes. Descripción comparativa de los genomas mitocondriales de la abeja melífera Apis (Hymenoptera: Apidae): cuatro nuevas secuencias genómicas y filogenia de Apis utilizando genomas enteros y genes individuales Se secuenciaron cuatro genomas mitocondriales completos (genomas mt) de miembros del género Apis (A. cerana, A. dorsata, A. laboriosa y A. mellifera ligustica). Estas cuatro y otras secuencias disponibles del genoma mt de Apis se utilizaron para examinar las características genómicas dentro del género, la disposición de los genes y las relaciones filogenéticas de Apis. Además, se evaluó el rendimiento filogenético de 15 genes individuales y dos combinaciones de genes concatenados para localizar genes adecuados para la filogenia de Apis. La reconstrucción filogenética usando todos los genes codificadores de proteínas concatenados (PCGs) y rRNAs apoyó fuertemente la presencia de tres linajes en Apis: los linajes hermanos de las abejas melíferas que anidan en las cavidades (A. cerana, A. mellifera, A. nigrocincta y A. koschevnikovi) y las abejas melíferas gigantes (A. dorsata y A. laboriosa), y un linaje divergente formado por las abejas melíferas enanas (A. florea y A. andreniformis). Los genomas mitocondrialas de Apis revelaron dos disposiciones génicas, trnE-trnS1 o trnS1-trnE en el bloque de tRNA en la región rica en A + T y la unión ND2. La disposición de genes encontrada en Apis es consistente con dos derivaciones independientes porque la misma disposición fue compartida entre especies no hermanas. Varias concatenaciones de dos genes, junto con el gen individual ND4, confirmaron la filogenia actual basada en el genoma mt entero con un apoyo relativamente fuerte, lo que significa que estas combinaciones de uno y dos genes son suficientes para una filogenia extendida dentro del gen de Apis, sin la inclusión de genes adicionales.