Xiao-Yu Kong

Control region translocation and a tRNA gene inversion in the mitogenome of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae)

Paraplagusia japonica (Cynoglossidae, Soleoidei) is characterized by a bilaterally asymmetrical and a series of fringes on the lips on the ocular side. Here we report for the first time the mitogenome of this tongue sole, which is 16,694 bp in length, and the gene order has been reorganized. The tRNA-Gln gene translocated from the light strand (L-strand) to the heavy strand (H-strand), accompanied by tRNA-Ile gene shuffling. In addition, the putative control region translocated downstream to the place between the ND1 and the tRNA-Gln genes, leaving a 26-bp trace fragment in the original position. Nevertheless, the rest gene order is identical to that of the typical fish. In addition, it is the first report of the rare ATT as an initiation codon for ND3, and the ATP6 ( − 26) and ND5 (+26) are unusually shorter or longer than those in other flatfish. These data will provide useful information for better understanding the molecular mechanisms of gene reorganization in fish mitogenome.

Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets

BackgroundIt can be seen from the available mollusk mitogenomes that the family Pectinidae exhibits the most variation in genome organization. In this study, comparative mitogenomic analyses were performed for three scallops from the subfamily Chlamydinae (Pectinidae), with the goal of characterizing the degree of variability of mitogenome organization and other characteristics among species from the same subfamily and exploring their possible evolution route.FindingsThe complete or nearly complete mtDNA sequences of scallop Mimachlamys nobilis (17 935 bp), Mizuhopecten yessoensis (20 964 bp) and Chlamys farreri (17 035 bp) were determined using long PCR amplification and primer walking sequencing strategy. Highly variable size difference of the three genomes resulted primarily from length and number variations of non-coding regions, and the major difference in gene content of the three scallop species are due to varying tRNA gene sets. Only 21, 16, and 17 tRNA genes were detected in the mitogenomes of M. nobilis, M. yessoensis and C. farreri, respectively. Remarkably, no trnS gene could be identified in any of the three scallops. A newly-detected trnA-like sequence within the mitogenome of M. yessoensis seems to exemplify the functional loss of a tRNA gene, and the duplication of trnD in M. yessoensis raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs. Analysis of putative evolutionary pathways of gene rearrangement indicates that transposition of neighboring gene blocks may play an important role in the evolution of mitogenomes in scallops. Parsimonious analysis of the genomic variations implies that the mitogenomes of M. yessoensis and C. farreri are likely to derive independently from a common ancestor that was closely related to M. nobilis.ConclusionComparative mitogenomic analyses among three species from the subfamily Chlamydinae show that the three genomes exhibit a high level of genomic variation and a diversity of tRNA gene sets, characterized by extensive translocation of genes. These features provide useful clues and information for evolutionary analysis of scallop mitogenomes.

Activator protein-1 (AP-1) and response to pathogen infection in the Hong Kong oyster (Crassostrea hongkongensis).

Growing evidence suggests that the transcription factor activator protein-1 (AP-1), a downstream target of mitogen-activated protein kinase (MAPK) signaling, plays a major role in stimulating the synthesis of immune effector molecules during innate immune responses. We have characterized ChAP-1, an AP-1-like protein in Crassostrea hongkongensis that is a member of the AP-1 family of proteins. ChAP-1 is composed of 290 amino acid residues with a Jun and bZIP domain at the N- and C-termini, respectively, a structure similar to that of known Ap-1 proteins. ChAP-1 mRNA is expressed in several tissues analyzed, with highest expression in the mantle. Expression of ChAP-1 increases in response to Vibrio alginolyticus, Salmo haemolyticus or Salmo cerevisiae infection and, despite the location of GFP-tagged full-length ChAP-1 protein in the cytoplasm, ChAP-1 activates the transcription of an L8G5-luc reporter gene, and its over-expression can also activate the AP-1-Luc reporter gene in HEK293T cells.

The complete mitochondrial genome of peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae) and comparative analysis of the control region among 13 soles

The complete mitogenome of the peacock sole Pardachirus pavoninus (Lacepède, 1802) was determined. The total length is 16536 bp, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes, as well as one control region (CR). The L-strand replication origin (OL), which is typically located in the WANCY cluster, is lost in P. pavoninus. The gene arrangement is identical to that in most teleosts. Comparison of the CR sequences among 13 soles reveals that a 211-bp fragment at the 5′-end of the CR is lost in the P. pavoninus mitogenome, responsible for its short sequence with a length of 872 bp. All typical conservative blocks (TAS, CSB-F, E, D, C, B, A, CSB-1, 2, 3) are identified. Seven out of 13 soles contain tandem repeats in the CR and the possible mechanisms of their formation are discussed. These results may provide the consensus sequences of the conserved units in the sole CR as well as molecular data for phylogenetic studies on Soleidae and Pleuronectiformes.

A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes).

BackgroundAlthough more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements.ResultsIn the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained.ConclusionsWe propose a “Double Replications and Random Loss” model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.

The complete mitochondrial genome of a striped sole Zebrias zebrinus (Pleuronectiformes: Soleidae)

Zebrias zebrinus belongs in the family Soleidae of Pleuronectiformes. There are overlaps in the ranges of identification characters between Z. zebrinus and another striped sole Z. fasciatus. In this study, the complete mitochondrial genome of Z. zebrinus was first determined. The total length was 16,758 bp, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations, and arrangements were identical to those of typical bony fishes. The overall base composition of the mitogenome was 28.7%, 30.0%, 15.2%, and 26.1% for A, C, G, and T, respectively, with an A+T content of 54.8%. This result would expect the contribution to the molecular identification of this species and further phylogenetic study of Soleidae and Pleuronectiformes.

Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes

BackgroundFew mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model.ResultsIn this study, the complete mitochondrial genomes of four flatfishes, Crossorhombus azureus (blue flounder), Grammatobothus krempfi, Pleuronichthys cornutus, and Platichthys stellatus were determined. A striking finding is that eight genes in the C. azureus mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the ND6 and seven tRNA genes (the Q, A, C, Y, S1, E, P genes) encoded by the L-strand have been translocated to a position between tRNA-T and tRNA-F though the original order of the genes is maintained.ConclusionsThese special features are used to suggest a mechanism for C. azureus mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes).

Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.

The complete mitochondrial genome sequence of Heteromycteris japonicus (Pleuronectiformes: Soleidae)

Abstract The bamboo sole Heteromycteris japonicus (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and a rostral hook. In this article, the complete mitochondrial genome sequence of this sole was first determined. The total length is 17,111 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12 S and 16 S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 29.2%, 27.5%, 16.3% and 27.1% for A, C, G and T, with a high A + T content (56.3%). The determination of H. japonicus mitogenome sequence could contribute to understanding the systematic evolution of the genus Heteromycteris and further phylogenetic study on Soleidae and Pleuronectiformes.

Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome

BackgroundTandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and deletion, however, remains unclear.ResultsWe analyzed DNA sequences of mt genome TRs (mtTRs) in the ridged-eye flounder (Pleuronichthys cornutus), and characterized DNA sequences of mtTRs from other vertebrates using the data available in GenBank. Tandem repeats are concentrated in the control regions; however, we found approximately 16.6% of the TRs elsewhere in the mt genome. The flounder mtTRs possess three motif types with hypervariable characteristics at the 3′ end of the control region (CR).ConclusionBased on our analysis of this larger dataset of mtTR sequences, we propose a novel model of Pause Melting Misalignment (PMM) to describe the birth and motif indel of tandem repeats. PMM is activated during a pause event in mitochondrial replication in which a dynamic competition between the nascent (N) heavy strand and the displaced (D) heavy strand may lead to the melting of the N-strand from the template (T) light strand. When mispairing occurs during rebinding of the N-strand, one or several motifs can be inserted or deleted in both strands during the next round of mt-replication or repair. This model can explain the characteristics of TRs in available vertebrate mt genomes.