Non-coding Control Region Research Articles

Phylogenetic analysis of BKV genetic variations, based on the whole sequence of the genome and different genomic sections.

BK polyomavirus (BKV) primarily infects humans in their early life stages, and in later life stages, immunosuppressed patients may develop asymptomatic infections. The nucleotides 1744-1812 in the VP1 gene are traditionally used to determine this virus's genotype. The complete genome of the BKVsamples from patients referred to Masih Daneshvari Hospital's Virology Research Center was amplified by previously known primer sets. The phylogenetic diversity of the whole genome, different genomic sections, and the noncoding control region of BKVsamples were investigated. Using software Mega X and references, the samples' genotype was determined in separate genomic fragments and the whole genome. The samples were classified into two genotypes (I and IV) and five subtypes (Ia, Ib-1, Ib-2, IVc-1, and IVc-2), but none of the isolates belonged to genotypes II, III, V, or VI. The large T antigen-based phylogenetic tree provided 100% bootstrap values for these divisions, which were superior to those (96%-100%) used in the VP1 sequence. Among the genomic segments, large tumor antigen and VP1 had the most mutations. The noncoding control area contained mutations at the O41 position in the granulocyte/macrophage stimulus gene and the P31 position in the NF-1 gene. The validity of the phylogenetic analysis was supported by sequence analysis, which found single-nucleotide polymorphisms(SNPs) that could be useful for subclassifying isolates. More research with a large number of samples and in the wider geographical areas is needed to understand the genetic diversity of the BKV in Iran and also to determine these SNPs' clinical significance in terms of patient outcome and viral load dynamics.

Complete mitochondrial genome analysis and molecular phylogenetic implications of Kennelia xylinana (Lepidoptera: Tortricidae).

Kennelia is a small genus in Tortricidae that is distributed in the Oriental and Palaearctic regions, and its taxonomic position within the subfamily Olethreutinae is controversial. For a comprehensive understanding of the genus, we sequenced the mitogenome of Kennelia xylinana, the type species of Kennelia, and Ancylis unculana, a species of Enarmoniini; analyzed the mitogenome characteristics of K. xylinana; and explored its phylogenetic position. Similar to other members of Lepidoptera, the mitogenome of K. xylinana is 15,762-bp long and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and a noncoding control region. In particular, we found a structure (TATAATTAATAA)11 in the middle of the AT-rich region. Based on the Bayesian inference and maximum likelihood analyses of the 13 PCGs of 40 tortricid species, representing 8 tribes of 2 subfamilies, K. xylinana was clustered with two members of Enarmoniini, A. unculana and Loboschiza koenigiana, and formed highly supported monophyly. The results indicate that Kennelia should be placed in the tribe Enarmoniini.

Characterization of the complete mitochondrial genome of Cerogria popularis Borchmann, 1936 (Coleoptera: Tenebrionidae)

In this study, we sequenced the complete mitochondrial genome (mitogenome) of Cerogria popularis Borchmann, 1936 based on the Illumina platform. The circular DNA molecule is 16,175 bp in size, including the 37 typical animal mitochondrial genes and a non-coding control region. All 37 genes are arranged in the same order as the previously reported most mitogenomes of Tenebrionidae. All PCGs initiate with standard start codon ATN (ATA/T/G/C) except cox1 with the special start codon AAT. Most PCGs terminate with TAA/G, whereas cox1, atp6, nad5, and nad4 end with its incomplete form T-. All the 22 tRNAs have the typical clover-leaf structure except for trnS1. The rrnL and rrnS genes are 1,250 and 737 bp in length, with an AT content of 82.6 and 84.5%, respectively. The phylogenetic tree supports the monophyly of the included tenebrionid subfamilies represented by more than one species. Furthermore, the sister relationship between Lagriinae and other tenebrionid subfamilies is recovered.

Sequencing and analysis of the complete mitochondrial genome of Gymnogobius laevis

Gymnogobius laevis (Steindachner, 1879) is a small, benthic freshwater fish. In a previous study, it was reported as a rare resident in Heilongjiang Province. In this study, the mitochondrial genome of G. laevis was sequenced. It is 16,519 base pairs (bp) in length and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and two non-coding control regions. The A + T content is 55.71% in the G. laevis mitochondrial genome. A phylogenetic tree shows that G. laevis is closely related to the family Gobiinae based on complete mitogenome sequences.

First mitogenome of Anthomyia illocata (Diptera, Anthomyiidae) yielded by next-generation sequencing

The mitochondrial genome of Anthomyia illocata Walker, 1857 belonging to the Anthomyiidae, was obtained using a next-generation sequencing approach. This 16,236 bp complete mitogenome consists of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes, as well as a non-coding control region. The Anthomyiidae are reconstructed as a paraphyletic group, with the genera Pegomya recovered as a sister group of the Scathophagidae.

Complete Mitochondrial Genomes of Five Racerunners (Lacertidae: Eremias) and Comparison with Other Lacertids: Insights into the Structure and Evolution of the Control Region.

Comparative studies on mitochondrial genomes (mitogenomes) as well as the structure and evolution of the mitochondrial control region are few in the Lacertidae family. Here, the complete mitogenomes of five individuals of Eremias scripta (2 individuals), Eremias nikolskii, Eremias szczerbaki, and Eremias yarkandensis were determined using next-generation sequencing and were compared with other lacertids available in GenBank. The circular mitogenomes comprised the standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and a long non-coding control region (CR). The extent of purifying selection was less pronounced for the COIII and ND2 genes in comparison with the rest of the PCGs. The codons encoding Leucine (CUN), Threonine, and Isolecucine were the three most frequently present. The secondary structure of rRNA of Lacertidae (herein, E. scripta KZL15 as an example) comprised four domains and 28 helices for 12S rRNA, with six domains and 50 helices for 16S rRNA. Five types and twenty-one subtypes of CR in Lacertidae were described by following the criteria of the presence and position of tandem repeats (TR), termination-associated sequence 1 (TAS1), termination-associated sequence 2 (TAS2), conserved sequence block 1 (CBS1), conserved sequence block 2 (CSB2), and conserved sequence block 3 (CSB3). The compositions of conserved structural elements in four genera, Acanthodactylus, Darevskia, Eremias, and Takydromus, were further explored in detail. The base composition of TAS2 – TATACATTAT in Lacertidae was updated. In addition, the motif “TAGCGGCTTTTTTG” of tandem repeats in Eremias and the motif ”GCGGCTT” in Takydromus were presented. Nucleotide lengths between CSB2 and CSB3 remained 35 bp in Eremias and Darevskia. The phylogenetic analyses of Lacertidae recovered the higher-level relationships among the three subfamilies and corroborated a hard polytomy in the Lacertinae phylogeny. The phylogenetic position of E. nikolskii challenged the monophyly of the subgenus Pareremias within Eremias. Some mismatches between the types of CR and their phylogeny demonstrated the complicated evolutionary signals of CR such as convergent evolution. These findings will promote research on the structure and evolution of the CR and highlight the need for more mitogenomes in Lacertidae.

Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species

Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as “ATGATAA”. Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).

Mitochondrial genomes of Sternochetus species (Coleoptera: Curculionidae) and the phylogenetic implications.

The three weevil species, Sternochetus gravis, S. mangiferae, and S. olivieri, have all been reported to be serious pests of mango fruits. Morphology, biology, and various management approaches of these economically important weevils have been well studied. However, no mitochondrial genomes have been reported from the genus Sternochetus. Herein, we assembled mitogenomes of all the three Sternochetus species to reveal their mitogenomic characteristics. A DNA library of 350 bp insert size was constructed and sequenced in Illumina's HiSeq6000 platform with a pair-end 150 bp sequencing strategy by Novogene. The sequence reads were assembled using GetOrganelle v1.7.1 and the genes were annotated by Geneious Prime 2021.0.3 and MITOS Web Server. Coupled with 61 published mitogenomes from 13 subfamilies of Curculionidae, we reconstructed phylogenetic trees to resolve evolutionary relationships of these closely related species and also examined subfamily-level classification among Curculionidae. All three mitogenomes are double-stranded circular molecules with 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 1 noncoding control region as in other insects. Higher interspecific nucleotide divergence (about 10%) of 13 PCGs indicated these three Sternochetus species diverged a long time ago. Phylogenetic analyses using both maximum likelihood and Bayesian inference methods showed that Sternochetus falls into the basal clade of Cryptorhynchini, a tribe in the subfamily Molytinae. The relationship of S. olivieri as a sister species to S. gravis + S. mangiferae was strongly supported. The monophyly of Cryptorhynchini was also well supported whereas Molytinae was suggested to be a polyphyletic group.

Three complete mitochondrial genomes of shortfin mako sharks, Isurus oxyrinchus, from the Atlantic and Pacific Oceans

We present complete mitogenome sequences of three shortfin mako sharks (Isurus oxyrinchus) sampled from the western Pacific, and eastern and western Atlantic oceans. Mitogenome sequence lengths ranged between 16,699 bp and 16,702 bp, and all three mitogenomes contained one non-coding control region, two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. Comparative assessment of five mitogenomes from globally distributed shortfin makos (the current three and two previously published mitogenomes) yielded 98.4% identity, with the protein-coding genes ATP8, ATP6, and ND5 as the most variable regions (sequence identities of 96.4%, 96.5%, and 97.6%, respectively). These mitogenome sequences contribute resources for assessing the genetic population dynamics of this endangered oceanic apex predator.

The complete mitochondrial genome of Pomadasys kaakan (Perciformes: Haemulidae)

Pomadasys kaakan (Cuvier 1830) is a fish found in coastal waters that is widely distributed in the Western Indo-Pacific Ocean and plays an important role in commercial fisheries. The complete mitochondrial genome of P. kaakan was determined for the first time in this study. The genome was 16,808 bp in length and consisted of 13 protein coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one noncoding control region. The overall base composition was estimated to be A: 27.1%; T: 24.7%; C: 31.7%; and G: 16.5%, with an AT bias of 51.8%. Molecular phylogenetic analysis suggested that P. kaakan was clustered with species of genera Plectorhinchus, Diagramma, and Parapristipoma, which also belonged to the Haemulidae family. Furthermore, the Haemulidae family was closely related to the group containing Oplegnathidae, Kyphosidae, Teraponidae, and Lutjanidae. These results may provide molecular information for the species evolution and phylogenetic status of P. kaakan in the suborder Percoidei.

Gene rearrangement in the mitogenome of whiteflies (Hemiptera: Aleyrodinae) along with their phylogeny and characterization of complete mitogenome of Aleurodicus rugioperculatus.

Mitochondrial genome rearrangements have been used for defining evolutionary relationships, but there have been incidences of convergences at different taxonomic levels. To gain new insights into whitefly mitogenome evolution, gene arrangement and phylogeny, we sequenced the complete mitogenome of Aleurodicus rugioperculatus (Aleyrodidae: Aleurodicinae) and conducted a comparative analysis with the previously published mitogenomes across the family Aleyrodidae. The complete mitogenome of Aleurodicus rugioperculatus was generated by Next generation sequencing method. It is 15,060bp circular molecule with 86.5A + T and 5.5% G + C content. It contains 37 genes (13 PCGs, two rRNAs, 22 tRNAs) and a non-coding control region (CR). Comparative analysis of codon usage indicated that the subfamily Aleyrodinae have weaker bias than Aleurodicinae. Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses yielded similar topologies supporting the monophyly of Aleyrodinae and Aleurodicinae. The gene order of 13 whiteflies was compared with ancestor to examine the plesiomorphies, synapomorphies and autapomorphies. We identified five gene blocks (I-V) in the whitefly ancestor that are shared plesiomorphies retained in different whitefly lineages. Gene block I is conserved in all whiteflies except three species. Conversely, we detected 83 derived gene boundaries within the family. Mapping these gene boundaries onto a phylogenetic tree revealed that 16 were symplesiomorphies for two subfamilies; 9 were synapomorphies between the species, and 28 autapomorphies for individual species. Comparative analyses of gene order of whiteflies revealed the derived gene boundaries which can be further investigated with more mitogenome data to examine the genome evolution in whiteflies.

Characterization of the complete mitochondrial genome of Takifugu pseudommus (Actinopterygii, Tetraodontidae)

The complete mitochondrial genome of Takifugu pseudommus was reported in the present study. It was 16,448 bp in length and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region. The nucleotide content of this genome was 29.91% for A, 29.09% for C, 15.20% for G, and 25.80% for T. The phylogenetic tree, constructed with complete mitochondrial genome, suggested T. pseudommus was closely related with T. chinensis, T. flavidus, and T. rubripes among Tetraodontidae species. This study could provide an important dataset for genetic diversity and species identification among the genus Takifugu.

Complete mitogenome of Antheraea formosana Sonan, 1937 (Lepidoptera: Saturniidae): an endemic silkmoth in Taiwan

The complete mitogenome of an endemic silkmoth in Taiwan, Antheraea formosana, was determined using Illumina next-generation sequencing. The mitogenome is 15,318 bp in length and consists of 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region. The overall base composition of the mitogenome showed a high A + T bias, and the A + T content (80.2%) was significantly higher than the G + C content (19.8%). All PCGs use the typical ATN as the initiation codon, with the exception of cox2, which begins with GTG, respectively. The complete mitogenome was used to reconstruct a phylogenetic tree, indicating that A. formosana is more closely related to Antheraea assamensis than other Antheraea species, with 93.19% nucleotide similarity.

The complete mitochondrial genome of Sarcophaga caerulescens (Diptera: Sarcophagidae)

Sarcophaga caerulescens (Zetterstedt 1838) (Diptera: Sarcophagidae) belongs to Sarcophagidae, which is closely associated with human life in ecological habits and has a clear environmental preference. Sarcophaga caerulescens can be better correlated with migration and postmortem interval (PMI) inference in forensic practice. In this study, we reported the complete mitochondrial genome (mitogenome) of S. caerulescens. The length of this mitogenome was 15,720 bp in total (GenBank accession No. MW551788), containing 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. Its nucleotide composition was A (39.7%), C (14.1%), G (9.4%), and T (36.9%). The phylogenetic relationships indicated that the species of S. caerulescens was closely related to S. similis. This study provides the mitochondrial data of S. caerulescens for further study of mitochondrial genome and enriches our understanding of the phylogenetic relationship of sarcophagid flies.

The complete mitochondrial genome of Artemia persimilis Piccinelli and Prosdocimi, 1968 (Crustacea: Anostraca)

In the study, we report the complete mitochondrial genome of Artemia persimilis Piccinelli and Prosdocimi, 1968 for the first time. The mitochondrial genome of A. persimilis is 15,436 bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes, and a non-coding control region (CR). Phylogenetic analysis showed that A. persimilis was at the basal position among the bisexual Artemia species, which revealed that A. persimilis is likely to be an ancestral clade. The present study could provide effective resources for population genetics study, as well as germplasm conservation in Artemia.

The phylogeny of the Anderson's White-bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes.

The phylogenetic structure of the genus Niviventer has been studied based on several individual mitochondrial and nuclear genes, but the results seem to be inconsistent. In order to clarify the phylogeny of Niviventer, we sequenced the complete mitochondrial genome of white‐bellied rat (Niviventer andersoni of the family Muridae) by next‐generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein‐coding genes (PCGs), two ribosomal RNA genes, and one noncoding control region (D‐Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6, and the entire mitogenome sequence except for the D‐loop revealed well‐resolved topologies supporting that N. andersoni was clustered with N. excelsior forming a sister division with N. confucianus, which statistically rejected the hypothesis based on the tree of cytochrome b (cytb) gene that N. confucianus is sister to N. fulvescens. Our research provides the first annotated complete mitochondrial genome of N. andersoni, extending the understanding about taxonomy and mitogenomic evolution of the genus Niviventer.

The first complete mitochondrial genome of the genus Dendronereis, represented by D. chipolini Hsueh, 2019 (Annelida, Nereididae) from Beibu Gulf, China

The genus Dendronereis Peters, 1854 is characterized in the polychaete family Nereididae by its feather-shaped branchiae on the anterior segments. In this study, we present the first complete mitogenome of Dendronereis, represented by D. chipolini Hsueh, 2019, collected from Beibu Gulf, China. The nucleotide composition is biased toward A + T nucleotides, accounting 31.5% for A, 22.3% for C, 14.7% for G and 31.5% for T. The assembled mitogenome is 15,763 bp in length, with a typical set of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and 1 non-coding control region. All genes are encoded on H-strand. The control region is 1260 bp in length and located between tRNA-Gly and tRNA-Met. Phylogenetic study showed that D. chipolini is arranged with high support into the clade of Namanereidinae. The complete mitogenome provides important molecular data for investigating the phylogeny and evolution of the nereid animals.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Eleutheronema rhadinum (Perciforms: Polynemidae)

This study aimed to elucidate the complete mitochondrial genome (mitogenome) of Eleutheronema rhadinum (Perciforms: Polynemidae). The circular mitogenome was 16,556 bp in size, with the base composition: A − 28.17%, T − 26.99%, C − 28.72%, and G − 16.12%. It had the typical vertebrate mitochondrial gene arrangement and was made up of 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes, and one non-coding control region. Phylogenetic analysis using maximum-likelihood approved that E. rhadinum belonged to the family Polynemidae and had close relationship to E. tetradactylum. The present data will contribute to future phylogenetic studies on members of family Polynemidae and conservation strategies for E. rhadinum.

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex.

Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568–16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

Diagnostic Value of JC Polyomavirus Viruria, Viremia, Serostatus and microRNA Expression in Multiple Sclerosis Patients Undergoing Immunosuppressive Treatment.

Markers of JC polyomavirus (JCPyV) activity can be used to evaluate the risk of progressive multifocal leukoencephalopathy (PML) in treated multiple sclerosis (MS) patients. The presence of JCPyV DNA and microRNA (miR-J1-5p), the anti-JCV index and the sequence of the non-coding control region (NCCR) in urine and plasma were determined in 42 MS subjects before treatment (T0), 6 months (T6) and 12 months (T12) after natalizumab, ocrelizumab, fingolimod or dimethyl-fumarate administration and in 25 healthy controls (HC). The number of MS patients with viruria increased from 43% at T0 to 100% at T12, whereas it remained similar for the HC group (35–40%). Viremia first occurred 6 months after treatment in MS patients and increased after 12 months, whereas it was absent in HC. The viral load in urine and plasma from the MS cohort increased over time, mostly pronounced in natalizumab-treated patients, whereas it persisted in HC. The archetypal NCCR was detected in all positive urine, whereas mutations were observed in plasma-derived NCCRs resulting in a more neurotropic variant. The prevalence and miR-J1-5p copy number in MS urine and plasma dropped after treatment, whereas they remained similar in HC specimens. Viruria and miR-J1-5p expression did not correlate with anti-JCV index. In conclusion, analyzing JCPyV DNA and miR-J1-5p levels may allow monitoring JCPyV activity and predicting MS patients at risk of developing PML.