Bp AT-rich Region Research Articles

Complete mitochondrial genome of Lasiommata deidamia and its phylogenetic implication to subfamily Satyrinae (Lepidoptera: Nymphalidae)

Lasiommata deidamia Eversmann taxonomically belongs to lepidopteran family Nymphalidae Rafinesque, 1815. The Complete mitochondrial genome (mitogenome) of the insect had been sequenced, with 15,244 bp of total length that has 81.12% AT content and contains a typical set of genes (13 protein-coding genes (PCGs), 22 tRNA genes and 2 rRNA genes) and a 417 bp AT-rich region. Another, 11 intergenic spacers (139 bp in total) and 16 overlaps (175 bp in total) have been founded. The longest interval is located between trnGln and nad2 while the maximum overlap is between trnHis and nad4. All PCG genes are started with the ATN codons and stop at TAA codons except cox1 which uses CGA as the initiation codon. No tandem repeat has been found in the AT-rich region. The phylogenetic tree inferred with Bayesian Inference based on all the 13 protein sequences of 45 mitogeomes reveals the phylogenetic relationships of the taxa in the subfamily Styrinae is (((Satyrini + Ypthimini) + (Amathusiini + Elymniini)) + Melanitini) and that within tribe Satyrini is ((((Lethina + Parargina) + Mycalesina) + Coenonymphina) +(Satyrina + (Melanargiina + Maniolina))).

Complete mitochondrial genome of Hypomecis punctinalis Scopoli, 1763 and its phylogenetic position within family Geometridae

Hypomecis punctinalis Scopoli, 1763 belongs to the Lepidopteran family Geometridae. We sequenced the complete mitochondrial genome (mitogenome) of H. punctinalis. The mitogenome is 15,648 bp long and contains a typical set of genes (13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes) and a 484 bp AT-rich region. All PCGs start with ATN codons and stop at TAA codon except for cox1 using CGA as initiation codon and nad4 and nad5 using incomplete termination codon T. Within the mitogenome, 17 intergenic spacers and seven overlaps are founded. The intergenic nucleotides are 294 bp in total and two longest intervals locate between trnGln and nad2 as well as trnCys and trnTyr . The overlap nucleotides are 47 bp in total and the maximum overlap lies between cox2 and trnLys . The AT-rich region of the mitogenome contains an ‘ATAGA + polyT’ motif, three copies of 30-bp-repeat and a short polyA tail. The phylogenetic tree shows the relationships of four subfamilies of Geometridae are (((Ennominae + Geometrinae)+Larentiinae)+Sterrhinae)) and the relationships within subfamily Ennominae are ((((Erannis+Biston)+(Jankowskia+(Hypomecis+(Apocheima+Milionia))))+Ectropis)+Abraxas)+Phthonandria)+Celenna).

Characterization of the complete mitochondrial genome of Neoasterolepisma foreli (Insecta: Zygentoma: Lepismatidae) and the phylogeny of basal Ectognatha

The silverfish Neoasterolepisma foreli belongs to the family Lepismatidae within Zygentoma and is well known for the peculiar habit of living in strict association with ant nests (myrmecophily). In this study, we describe its mitochondrial genome, a circular molecule of 15,398 bp including the canonical 13 PCGs, 22 tRNAs, 2 rRNAs, as well as a 403 bp AT-rich region. A phylomitogenomic analysis of the new sequence, alongside basal hexapod mtDNAs, confirmed the monophyly of all orders, with some uncertainty over the position of the enigmatic Tricholepidion gertschi that would make Zygentoma paraphyletic. Neoasterolepisma foreli is recovered in a basal position within family Lepismatidae, at odd with our current understanding of the group that would, in turn, suggest a closer relationship with the genus Lepisma (Mendes, 1991).

Complete mitochondrial genome and phylogenetic position of the Eastern Asian species, Promalactis odaiensis (Lepidoptera: Gelechioidea: Oecophoridae)

The complete mitochondrial genome of Promalactis odaiensis is described in this study. The mitogenome is 15,733 base pairs with 13 protein coding genes (PCGs), 2 rRNAs, 22 tRNAs, and a 679 bp AT-rich region. The overall base composition was 79.43% AT and 20.57% GC. Among 13 PCGs, eleven genes (Nad2, Atp8, Atp6, Cox3, Nad3, Nad5, Nad4, Nad4L, Nad6, CYTB, and Nad1) harbour the typical stop codon TAA or TAG, whereas remaining two genes (Cox1, Cox2) terminated with T.

Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae).

In the present study, the complete mitogenome of Theretra japonica was sequenced and compared with other sequenced mitogenomes of Sphingidae species. The mitogenome of T. japonica, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) and a region rich in adenine and thymine (AT-rich region), is a circular molecule with 15,399 base pairs (bp) in length. The order and orientation of the genes in the mitogenome are similar to those of other sequenced mitogenomes of Sphingidae species. All 13 protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome C oxidase subunit 1 gene (cox1) which is initiated by the codon CGA as observed in other lepidopteran insects. Cytochrome C oxidase subunit 2 gene (cox2) has the incomplete termination codon T and NADH dehydrogenase subunit 1 gene (nad1) terminates with TAG while the remainder terminates with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Ile and Leu2 are the most frequently used codon families and codons CGG, CGC, CCG, CAG, and AGG are absent. The 431 bp AT-rich region includes the motif ATAGA followed by a 23 bp poly-T stretch, short tandem repeats (STRs) of TC and TA, two copies of a 28 bp repeat ‘ATTAAATTAATAAATTAA TATATTAATA’ and a poly-A element. Phylogenetic analyses within Sphingidae confirmed that T. japonica belongs to the Macroglossinae and showed that the phylogenetic relationship of T. japonica is closer to Ampelophaga rubiginosa than Daphnis nerii. Phylogenetic analyses within Theretra demonstrate that T. japonica, T. jugurtha, T. suffusa, and T. capensis are clustered into one clade.

The complete mitochondrial genome of the Sideridis albicosta (Lepidoptera: Noctuoidea: Noctuidae)

The complete mitochondrial genome (mitogenome) of Sideridis albicosta is described in this study. The circular molecule is 15,320 bp in length and contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one AT-rich region. Thirteen PCGs is 11,252 bp in total, encoding 3723 amino acids. All PCGs start with ATN, except for COI gene starting with CGA; 10 of the 13 PCGs use the typical stop codon TAA, whereas COI, COII, and ND4 stop with a single T. The rrnL and rrnS genes are 1377 bp and 783 bp in length, respectively. The 328 bp AT-rich region contains several structures characteristic of the lepidopterans. New phylogenetic analyses upon mitogenomics would provide us further insights on the taxonomy and phylogeny of Noctuoidea.

The complete mitochondrial genome of comma, polygonia c-aureum (Lepidoptera: Nymphalidae: Nymphalinae)

The mitochondrial genome (mitogenome) of Polygonia c-aureum (Lepidoptera: Nymphalidae: Nymphalinae) is determined to be 15,209 bp in length and shows AT bias (80.6%). Similar to other butterflies, it contains 37 typical mitochondrial genes and one AT-rich region (D-loop). All protein-coding genes (PCGs) started with ATN, except for cox1 gene with CGA(R), which is often found in other butterflies, and seven PCGs harbour the typical stop codon TAA, whereas cox1, cox2, nad3, nad5, nad4 and nad1 end with a single T. The rrnL and rrnS genes are 1332 bp and 773 bp in length, respectively. The 342 bp AT-rich region contains non-repetitive sequences, but harbour several features common to the lepidopterans, including the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element preceded by the ATTTA motif. The complete mitogenome sequence provided here would be useful for further understanding the taxonomy and phylogeny of Nymphalinae.

Assembly of the mitochondrial genome of the hydrothermal vent crab Segonzacia mesatlantica and detection of potential nuclear pseudogenes

We assembled the mitogenome of the Bythograeid crab Segonzacia mesatlantica, using long-range amplification of the mitochondrial genome. The mitogenome is 15,521 base pair long (33.8% A, 21.7% C, 10.5% G, 34% T) with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a 624 bp AT-rich region. The gene arrangement is similar to other Brachyuran species. A whole genome shotgun sequencing approach revealed the presence of mitochondrial pseudogenes in the nuclear genome. This fifth mitogenome for a species of Bythograeidae should help resolve the puzzling question of the evolutionary origin of a family limited to deep-sea hydrothermal vents.

Complete mitochondrial genome of the soybean stem fly Melanagromyza sojae (Diptera: Agromyzidae)

We report the complete mitochondrial DNA genome of the soybean stem fly (SSF) Melanagromyza sojae from Brazil Santa Catarina state based on Illumina MiSeq sequence data. The estimated mitogenome is 15 475 base pairs (bp) (KT597923), with 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 tRNAs, and an estimated 579 bp AT-rich control region. Similar to other insects, the SSF mitogenome is A–T bias with 40.9% A, 36.7% T, 13.6% C, and 8.8% G. Molecular characterization of SSF mitogenome will facilitate the development of effective molecular markers, and robust and rapid identification of suspected biosecurity incursions and field infestations of this insect pest.

The Complete Mitochondrial Genome of the Beet Webworm, Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications.

The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.9%, and the AT skewness is slightly negative (-0.023). All PCGs start with the typical ATN codons, except for COX1, which may start with the CGA codon. Nine of 13 PCGs have the common stop codon TAA; however, COX1, COX2 and ND5 utilize the T nucleotide and ND4 utilizes TA nucleotides as incomplete termination codons. All tRNAs genes are folded into the typical cloverleaf structure of mitochondrial tRNAs, except for the tRNASer(AGY) gene, in which the DHU arm fails to form a stable stem-loop structure. A total of 157 bp intergenic spacers are scattered in 17 regions. The overlapping sequences are 42 bp in total and found in eight different locations. The 329 bp AT-rich region is comprised of non-repetitive sequences, including the motif ATAG, which is followed by a 14 bp poly-T stretch, a (AT11 microsatellite-like repeat, which is adjacent to the motif ATTTA, and a 9 bp poly-A, which is immediately upstream from the tRNAMet gene. Phylogenetic analysis, based on 13 PCGs and 13 PCGs+2 rRNAs using Bayesian inference and Maximum likelihood methods, show that the classification position of Pyraloidea is inconsistent with the traditional classification. Hesperioidea is placed within the Papilionoidea rather than as a sister group to it. The Pyraloidea is placed within the Macrolepidoptera with other superfamilies instead of the Papilionoidea.

The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae)

In this study, the complete mitochondrial genome sequence of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) has been reported for the first time. The total length of the mitogenome was 15,659 bp with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with CGA codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All tRNAs have typical structures of insect mitochondrial tRNAs. The 494 bp AT-rich region contains several features common to other lepidopterans, such as some structures of repeated motifs and microsatellite-like elements and a poly-A element upstream of transfer RNA M (trnM) gene.

The complete mitochondrial genome of Bombyx mori strain Huayu (Lepidoptera: Bombycidae)

The complete mitochondrial genome of Bombyx mori strain Huayu (Lepidoptera: Bombycidae) is determined in this study. The genome was 15,666 bp long, with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with uncertained codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All tRNAs have typical structures of insect mitochondrial tRNAs. The 494 bp AT-rich region contains several features common to other lepidopterans, such as the motif ATAGA followed by an 18 bp poly-T stretch and an 11 bp poly-A element upstream of transfer RNA M (trnM) gene.

The complete mitochondrial genome of Bombyx mori strain Baiyun (Lepidoptera: Bombycidae)

The complete mitochondrial genome of Bombyx mori strain Baiyun (Lepidoptera: Bombycidae) was determined in this study. The genome was 15,629 bp long with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with CGA codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All the tRNA genes showed typical secondary cloverleaf structures. The 496 bp AT-rich region contains several features common to other lepidopterans, such as the motif ATAGA followed by an 18-bp poly-T stretch and two microsatellite-like (TA)8 and (AT)9 elements preceded by the ATTTA motif.

The complete mitochondrial genome of Callerebia suroia (Lepidoptera: Nymphalidae: Satyrinae)

The complete mitochondrial genome (mitogenome) of Callerebia suroia (Lepidoptera: Nymphalidae: Satyrinae) was determined and analyzed in this paper. The circular genome is 15,208 bp long, including 37 typical mitochondrial genes and one non-coding AT-rich region. All protein-coding genes (PCGs) started with ATN, except for COI gene with CGA(R), which is often found in other butterflies; nine PCGs harbor the typical stop codon TAA, whereas COI, COII, ND5 and ND4 end with a single T. All tRNA genes display typical secondary clover-leaf structures, except for tRNASer(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop. The lrRNA and srRNA genes are 1,347 bp and 753 bp in length, with their AT contents of 84.4% and 85.4%, respectively. The 417 bp AT-rich region contains non repetitive sequences, but harbor several features common to the lepidopterans, including the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element preceded by the ATTTA motif.

The complete mitochondrial genome of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae)

The complete mitochondrial genome (mitogenome) sequence of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae) was determined in this study. The mitogenome is 15,143 bp in length, containing 37 typical animal mitochondrial genes: 13 putative protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene content and order are identical to those of other lepidopteran mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI gene which uses CGA as its start codon. Nine PCGs terminate in the common stop TAA, whereas the COI, COII, ND5 and ND4 genes end with single T. All tRNA genes showed typical secondary cloverleaf structures except for the tRNASer(AGN), which has a simple loop with the absence of its DHU stem. The 316 bp AT-rich region contains several features common to the other lepidopterans, such as the motif ATAGA followed by an 19-bp poly-T stretch and two microsatellite-like (TA)8(AT) and (TA)4 elements preceded by the ATTTA motif.

Complete mitogenome of the Lesser Purple Emperor <I>Apatura ilia</I> (Lepidoptera: Nymphalidae: Apaturinae) and comparison with other nymphalid butterflies

The complete mitochondrial genome of Apatura ilia (GenBank accession no. JF437925) was determined as a circular DNA molecule of 15 242 bp, with common genes of 13 putative proteins, 2 rRNAs, and 22 tRNAs and of the same gene arrangement as in other sequenced lepidopterans. All protein-coding genes had the typical start codon ATN, except for the COI's using CGA as its start codon as previously demonstrated in other lepidopteran species. The comparison of the nucleotide sequences of the A. ilia mitogenome with ten other Nymphalidae species showed nearly identical gene orientation and arrangement, with only a few alterations in non-coding fragments. The nucleotide composition and codon frequency all fell into the range estimated for the order Lepidoptera. The A. ilia mitochondrial genome had the canonical set of 22 tRNA genes folded in the typical cloverleaf structure, with an unique exception of tRNA(Ser) (AGN). The mitochondrial genes from A. ilia were overlapped in a total of 33 bp at 9 locations, as well as interleaved with a total of 155 bp intergenic spacers, spread over 12 regions with the size ranging from 1 to 49 bp. Furthermore, the spacer between ND6 and Cyt b harbored a microsatellite-like repeat (TA)(23) not found in other completely sequenced nymphalid genomes. The 403 bp AT-rich region harbored two conserved motifs (ATAGA, ATTTA), a 21 bp polyT stretch, a 10 bp poly-A region, along with two microsatellite-like repeats ( (TA)(10) and (TA)(7)), as detected in other nymphalid butterflies.

Cloning of a regulatory gene fromStreptomyces cattleya and study on itscis-acting element

Primers were designed from the highly conserved protein regions of luxl, one of the two component regulatory genes in prokaryotic, and an about 180 bp DNA from Streptomyces cattleya was amplified by PCR. Using this fragment as a probe, Southern hybridization was accomplished with chromosome DNA of S. cattleya, leading to the cloning of the foreign DNA into pBluescript (SK-). DNA sequencing and frame analysis showed an intact ORF consisting of 1800 bp; the G+C composition was 69.3%. Upstream from the ORF was a 249 bp AT rich region, downstream of the ORF several complicated secondary structures were found. DNA-binding assay by gel retardation demonstrated the presence of a protein that specifically bound to the 249 bp AT rich region. The region also showed anomalous electrophoretic mobility at low temperature, like that of a bent DNA molecule, indicating that the region contains a cis-acting element.

Positive cis-acting regulatory sequences mediate proper control of POL1 transcription in Saccharomyces cerevisiae.

The 5'ACGCGT3' MluI motif, which is found in the upstream region of several yeast DNA-synthesis genes which are periodically expressed during the mitotic cell-cycle, is present twice in the 5' non-coding region of the DNA-polymerase alpha gene (POL1). Deletion of the most distal repeat does not affect POL1 transcription, while the adjacent 40 base-pair (bp) downstream sequence is necessary both for the proper level and the fluctuation of POL1 mRNA. This region contains the 5'ACGCGTCGCGT3' sequence, which is sufficient to control periodic transcription of a CYC1-lacZ reporter gene with the same kinetics observed for POL1. The adjacent 29 bp AT-rich region does not show any activity by itself, but it acts synergistically in conjunction with at least one MluI hexamer to stimulate CYC1-lacZ expression. By further deletion analysis, DNA sequences necessary to initiate POL1 transcription at the proper sites have also been identified.

Sequence of the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase from a gymnosperm, Douglas fir

The chloroplast rbcL gene encodes the large subunit ofribulose 1,5-bisphosphate carboxylase [ 3 ], the enzyme that catalyzes CO 2 fixation during photosynthesis [6]. rbcL nucleotide sequences data have been used extensively, and proven to be quite powerful, in studies of plant phylogeny and molecular evolution [9, 10]. Complete sequences have been determined from several monocotyledonous and dicotyledonous angiosperms, algae, photosynthetic bacteria, and a bryophyte [7, 9, 10]. We report here an rbcL gene sequence from a Pinaceous gymnosperm, Douglas fir (Pseudotsuga menziesii (Mirb.) Franco). rbcL was sequenced by the dideoxynucleotide chain termination method using recombinant plasmid DNA as the template [2]. In addition to the 1425 base pair (bp) coding region, we sequenced 251 bp upstream and 179bp downstream of the open reading frame (Fig. 1). The coding region has an inferred amino acid sequence that is 93.0% similar to tobacco [4], 90.3% to maize [5, 8], and 92 .4~ to liverwort [7]; its DNA sequence is 85.8%, 83.8%, and 82.6 % similar, respectively. There is a deletion of one codon and an insertion of one codon in the Douglas fir sequence relative to maize, and a deletion of two codons relative to tobacco. The 5' flanking region contains prokaryoticlike consensus promoter sequences and ribosome binding site. Possible 35 (TTGCAT) and 10 (TACAAT) regions are located at positions 80 to 85 and 103 to 108, respectively (underlined in Fig. 1) and are separated by a 17 bp AT-rich region. The Douglas fir rbcL 35 sequence differs in two nucleotide positions from angiosperm sequences (TTGCAT instead of TTGCGC) [4, 10]. The putative ribosome binding site [1] is also underlined, and located at nucleotides 242 to 246. Two likely stem-loop transcription termination structures [ 10] are present in the 3' flanking region (horizontal arrows in Fig. 1).

DNA-directed oligomerization of the monomeric Ner repressor from the Mu-like bacteriophage D108.

We have purified the 8.6 kd ner gene product (a lambda Cro-like protein which negatively regulates transcription from two divergent and overlapping promoters) from the Mu-like transposable bacteriophage D108. Chemical and enzymatic protection experiments show the D108 ner-operator to contain two perfect 11 bp (5'-CCG-TGAGCTAC-3') inverted repeats separated by an 8 bp AT-rich region. Ner makes base-specific contacts in the major groove spanning the 11 bp repeats and also interacts with regions flanking these sites such that its operator comprises five turns of the DNA helix. Furthermore, gel filtration chromatography and dimethyl suberimidate crosslinking experiments indicate that D108 Ner (at concentrations exceeding 5 microM) is a monomer in solution, yet crosslinks as a dimer when bound to its operator site. As a small (73 amino acids) monomeric protein, Ner does not display strong homology with any known DNA-binding proteins. By virtue of the interactions with its operator it appears to bind DNA in a markedly different manner from other known prokaryotic repressors thus adding to the growing catalog of protein motifs used for specific binding to DNA.