Non-coding AT-rich Region Research Articles

The complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae)

In this study, the complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae) has been reported for the first time. It was a circular molecule of 15,648 bp in length, containing 37 typical coding genes and one non-coding AT-rich region. The overall composition of the mitogenome was A (43.05%), G (7.30%), C (11.35%), and T (38.29%). Its gene order and content were identical to the common type found in most insect mitogenomes. All protein coding genes (PCGs) started with a typical ATN initiation codon, except for the cox1 gene, which began with CGA codon. Eleven genes used standard complete termination codon TAA, whereas the cox1 and cox2 genes ended with single T. All tRNA genes displayed typical secondary cloverleaf structures as those of other insects. Additionally, the 494 bp long AT-rich region contained several structures common to the other lepidopterons, such as some structures of repeated motifs and microsatellite-like elements.

The complete mitochondrial genome of Graphium chironides (Lepidoptera: Papilionidae: Papilioninae)

The complete mitochondrial genome (mitogenome) of Graphium chironides is a circular molecule of 15,235 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a non-coding AT-rich region. All PCGs start with a typical ATN initiation codon, except for COI, which is initiated with the CGA codon as observed in other butterfly species. Eleven PCGs terminate in the complete stop codon TAA or TAG, whereas the COI and COII genes end with single T. Twelve intergenic spacers (79 bp in total) and 15 overlapping regions (42 bp in total) are dispersed throughout the whole genome. The two rRNA genes (lrRNA and srRNA) are 1343 bp and 778 bp in size, with the AT contents of 84.2% and 85.3%, respectively. All tRNA genes display typical secondary cloverleaf structures except for tRNASer(AGN) which loses the DHU arm. The 419 bp long AT-rich region contains several features common to the other lepidopterans, such as the ATAGA motif followed by a 12 bp poly-T stretch, two microsatellite-likes (TA)7 and (TA)9 preceded by the ATTTA motif.

The complete mitochondrial genome of the Chrysoperla sinica (Tjeder)

The complete mitochondrial genome of the Chrysoperla sinica was sequenced in this study. It is 16,057 bp in length, and contains 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 rRNA genes and 1 non-coding AT-rich region. But, C. sinica lack long tandem repeats. The Chrysoperla sinica mitogenome displays a very high level of similarity (99.27%) with Chrysoperla nipponensis. The genome base composition is 39.24% A, 39.70% T, 11.98% C, and 9.08% G. Similar to other insects, all PCGs are initiated by a typical ATN codon, except COX1, which starts with TCG. Nine PCGs have the standard, complete stop codon (TAA or TAG), and the other four PCGs end with the incomplete stop codon (TA or T).

The complete mitogenome of the minute mudskipper, Periophthalmus minutus Eggert, 1935 (Perciformes: Gobiidae: Oxudercinae)

The mitogenome of an Australian sample of the mudskipper, Periophthalmus minutus, was recovered from partial sequencing using the MiSeq sequencer. This mudskipper has a mitogenome of 16,506 base pairs (55% A + T content) made up of two ribosomal subunit genes, 13 protein-coding genes, 22 transfer RNAs, and a 838 bp non-coding AT-rich region. This is the first sequenced mitogenome for the genus Periophthalmus and the fifth for the subfamily Oxudercinae.

The complete mitochondrial genome of the bass yabby Trypaea australiensis Dana 1852, (Crustacea; Decapoda; Callianassidae) – a new gene order for the Decapoda

The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.

The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea)

The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.

RETRACTED ARTICLE: The complete mitochondrial genome of the tobacco budworm, Helicoverpa assulta

The complete mitochondrial genome of the tobacco budworm Helicoverpa assulta was sequenced. It is 15,351 bp in length, and contains 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 rRNA genes and a non-coding AT-rich region. The H. assulta mitogenome displays a very high level of identity (99.76%) with Helicoverpa armigera. The genome base composition is 40.50% A, 40.40% T, 11.32% C and 7.70% G. Similar to other Lepidoptera insects, all PCGs are initiated by a typical ATN codon, except CO1, which starts with CGA. Nine PCGs have the standard, complete stop codon (TAA), and the other four PCGs end with the incomplete stop codon TA–.

The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura)

The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.

The complete mitochondrial genome of the Colletes gigas (Hymenoptera: Colletidae: Colletinae)

The complete mitochondrial genome of the Colletes gigas (Hymenoptera: Colletidae) is determined to be 15,885 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a major non-coding AT-rich region. All PCGs initiate with typical ATN codons and end with the complete termination codon TAA, except for the cob gene, which harbors the stop codon of TAG. Twenty-four intergenic spacers (614 bp in total) and 7 overlapping regions (37 bp in total) are dispersed throughout the whole genome. The non-coding AT-rich region is 539 bp long and contains a tandem repeat region, which has also been reported in other insects. This is the first completely sequenced mitochondrial genome of the family Colletidae.

The complete mitochondrial genome sequence of Helicophagella melanura (Diptera: Sarcophagidae)

The mitochondrial genome of Helicophagella melanura, a representative of the Sarcophagidae family, was completely sequenced for the first time. The genome is a double-stranded circular molecule of 15,190 bp length, including the 37 genes and 1 non-coding AT-rich region. The gene contents of the mtDNA were identical to those observed in the ancestral arthropod. The total base composition of Helicophagella melanura mitochondrial genome is 39.42% for A, 36.22% for T, 14.71% for C and 9.65% for G and in the order A > T > C > G. The mitochondrial genome data of Helicophagella melanura is useful markers for species discrimination in forensic entomology and for phylogenetic analysis.

The complete mitochondrial genome of the Neochauliodes fraternus (Megaloptera: Corydalidae)

The mitochondrial genome of Neochauliodes fraternus (Megaloptera: Corydalidae) is a circular molecule of 15,768 bp in length, containing 37 typical mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most insect mitogenomes. All PCGs start with a typical ATN codon except for the ND1 which uses TTG as its start codon; all PCGs terminate in the common stop codon TAA or TAG, except for the COI, COIII, ND3, ND5, ND4 and CYTB which use single T as their stop codons. The non-coding AT-rich region is 1031 bp long, located between rrnS and tRNAlle genes. It contains some structures of repeated motifs and microsatellite-like elements characteristic of the megaloptera.

The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae)

The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.

The complete mitogenome of the ghost crab Ocypode ceratophthalmus (Pallas, 1772) (Crustacea: Decapoda: Ocypodidae)

The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.

The complete mitochondria genome of Ravinia pernix (Diptera: Sarcophagidae)

Ravinia pernix is considered to be a forensically important fly species of the family Sarcophagidae. In this study, we present the complete mitochondrial genome of Ravinia pernix for the first time. There is one encoding region including 37 genes and one non-coding AT-rich region observed in the 15,778 bp circular genome, containing 13 protein-encoding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The arrangement of the genes is the same as that found in the ancestral arthropod. The base compositions of A, T, G and C are 39.57%, 37.60%, 9.36% and 13.47%, respectively. The mitochondrial genome of Ravinia pernix presented will be valuable and useful for enriching the dipteran mitochondrial genomes, resolving phylogenetic relationships within the family Sarcophagidae and the order Diptera, and providing a molecular tool for species identifications for forensic purposes.

The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca)

The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.

The Complete mitochondrial genome of the Neochauliodes rotundatus (Megaloptera: Corydalidae)

The mitochondrial genome of Neochauliodes rotundatus (Megaloptera: Corydalidae) is a circular molecule of 15,774 bp in length, containing 37 typical mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most insect mitogenomes. All PCGs start with a typical ATN codon except for the ND1 which uses TTG as its start codon; all PCGs terminate in the common stop codon TAA or TAG, except for the COI, COIII, ND3, ND5, ND4 and CYTB which use single T as their stop codons. The 1061 bp non-coding AT-rich region is located between rrnS and tRNAlle genes, containing some structures of repeated motifs and microsatellite-like elements characteristic of the Megaloptera insects.

The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae)

The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.

The complete mitochondrial genome of Myrmeleon immanis Walker, 1853 (Neuroptera: Myrmeleontidae)

In this study, the complete mitochondrial genome sequence of Myrmeleon immanis Walker, 1853 (Neuroptera: Myrmeleontidae) has been obtained with PCR, which is a circular molecule of 15,802 bp in length, contains 37 typical mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. The nucleotide composition is biased toward A and T as in most other insects. The A + T content of the whole genome, PCGs, tRNAs, rRNAs and the control region is 75.6%, 74.3%, 73.6%, 76.2%, 79.6%. All PCGs start with a typical ATN codon except for the COI which uses ACG as its start codon; all PCGs terminate in the common stop codon TAA or TAG, except for the COI, COII which use single T as their stop codons.

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 Hemiodoecus leai (Hemiptera: Coleorrhyncha: Peloridiidae)

The mitochondrial genome of Hemiodoecus leai (Hemiptera: Coleorrhyncha: Peloridiidae) was determined and annotated. The entire genome was 15,949 bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and an A + T-rich region. The genome has a gene arrangement identical to the inferred ancestral insects. Twelve of the 13 PCGs initiate with the standard start codons ATN, whereas CO1 starts with CGA. The tRNAs have be folded into typical cloverleaf secondary structures, except that the stem of the DHU arm was absent in tRNASer(GCT). The non-coding AT-rich region is 1414 bp long and is located between the rrnS and tRNAlle genes. The complete mitogenome sequence of H. leai could provide fundamental data for the phylogenetic and biogeographic studies of the Peloriidae as well as the Coleorrhyncha and Hemiptera.