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Xiao-yu Kong - One of the best experts on this subject based on the ideXlab platform.
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the complete mitochondrial genome sequence of cynoglossus roulei Pleuronectiformes cynoglossidae
Mitochondrial DNA Part B, 2019Co-Authors: Shixi Chen, Wei Shi, Hairong Luo, Jiangxing Dong, Xiao-yu KongAbstract:The complete mitogenome of Cynoglossus roulei is 16,598 bp in length, containing 37 genes, among them, ND6 and eight tRNA genes are encoded by L-strand and other genes by H-strand, which are as sam...
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the complete mitochondrial genome sequence of asterorhombus intermedius Pleuronectiformes bothidae
Mitochondrial DNA Part B, 2019Co-Authors: Shixi Chen, Wei Shi, Hairong Luo, Xiao-yu KongAbstract:The complete mitogenome of Asterorhombus intermedius is 16,886 bp in length, containing 37 genes, among them, ND6 and eight tRNA genes are encoded by L-strand, and other genes by H-strand, which ar...
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Remarkable sequence polymorphisms in 18S rDNA of Pleuronichthys cornutus (Pleuronectiformes: Pleuronectidae).
Gene, 2018Co-Authors: Min Yang, Wei Shi, Xiao-yu Kong, Li Gong, Hairong LuoAbstract:Abstract Highly conserved 18S rDNA sequences encode ribosomal RNA and evolve in a concerted manner. In this study, 178 sequences of 18S rDNA from the ridge-eyed flounder, Pleuronichthys cornutus, were analyzed. The total sequences yielded five distinguishable types of 18S rDNA—A, B, R, S, and L—that were defined based on sequence alignments, clone clustering, and recombination detection. The length of 176 clones ranged from 1838 bp to 1846 bp, with one particularly short clone reaching only 1466 bp and one long clone reaching up to1869 bp. As per current criteria for pseudogene inference, Type S was inferred to be a pseudogene due to its truncated length (380 bp) and low minimum free energy (−536.9 kcal·mol−1). Type L had a unique 20-bp insertion and was also predicted to be as a pseudogene. Types A and B showed 31 differential sites, which in Type A was consistent with 18S rDNA sequences found in six other flounders, while Type B and recombinant Type R were not. Maximum K2P genetic distances were calculated within Type B (0.0232) and R (0.0313); these were much higher than that of Type A (0.0093) or between the six flounders (0.011). Only Type A was detected by reverse transcription experiments and linked to functional ITS1 and 5.8S fragments; Types B and R were linked to both functional and pseudo genes. Accordingly, Type A is likely the functional gene, and Types B and R are probable pseudogenes. The heterogeneity of the five types revealed that 18S rDNA sequences evolved in a non-concerted evolution manner in P. cornutus. Furthermore, our results suggest that more features should be used to identify functional or pseudo genes.
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the complete mitochondrial genome of pseudaesopia japonica Pleuronectiformes soleidae
Mitochondrial DNA, 2017Co-Authors: Li Gong, Wei Shi, Min Yang, Xiao-yu KongAbstract:The Pseudaesopia japonica belongs to family Soleidae in order Pleuronectiformes. In this study, the complete mitochondrial genome of P. japonica was determined and described. The mitogenome is 16 790 bp in length and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs, one control region, and a light strand replication origin. The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 28.5%, 25.7%, 30.3%, and 15.5%, for A, T, C, and G, respectively, with a slight bias on A + T content (54.3%). The maximum likelihood phylogeny tree of 22 flatfishes demonstrated that the species from Zebrias and Aesopia firstly formed a sister group, and then clustered in the same clade with P. japonicas. This study is expected to contributing to the systematic evolution of P. japonicas and further phylogenetic relationship of Soleidae and Pleuronectiformes.
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non concerted evolution in ribosomal its2 sequence in cynoglossus zanzibarensis Pleuronectiformes cynoglossidae
Biochemical Systematics and Ecology, 2016Co-Authors: Li Gong, Wei Shi, Min Yang, Xiao-yu KongAbstract:The nuclear ribosomal RNA genes (nrDNA) include three rRNA genes (18S, 5.8S, and 28S) and two internal transcribed spacers (ITS1 and ITS2). The lack of variability in nrDNA has been explained as the result of concerted evolution. In fact, many examples of variation have been discovered, suggesting a non-concerted evolution process. There are few studies on ITS2 in teleostean fishes; particularly no reports on flatfishes. In this study, we focused on ITS2 in Zanzibar tonguesole, Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae). Three types of ITS2 sequences (Type A, B, and C) coexisted and mainly differ in length, nucleotide diversity (π), secondary structure, and minimum free energy. Based on these different features, Type B and C were speculated as the putative pseudogenic ITS2 region. Moreover, Type C sequences were detected as recombinant from crossing over between Type A and B sequences. To our knowledge, this is the first report on ITS2 recombination in animal ribosomal RNA genes. The high degree of ITS2 sequence polymorphism at the intraindividual level supported a non-concerted evolution pattern in the C. zanzibarensis genome. These results provide useful data for further studies on ITS2 in flatfishes and contribute to polymorphism analyses of ribosomal RNA genes in teleostean fishes.
Wei Shi - One of the best experts on this subject based on the ideXlab platform.
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variations in the conserved 18s and 5 8s reveal the putative pseudogenes in 18s its1 5 8s rdna of cynoglossus melampetalus Pleuronectiformes cynoglossidae
Biochemical and Biophysical Research Communications, 2021Co-Authors: Wei Shi, Min Yang, Li Gong, Hairong LuoAbstract:Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.
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novel gene rearrangement pattern in cynoglossus melampetalus mitochondrial genome new gene order in genus cynoglossus Pleuronectiformes cynoglossidae
International Journal of Biological Macromolecules, 2020Co-Authors: Li Gong, Wei Shi, Hairong Luo, Ying Zhang, Liqin Liu, Bingjian Liu, Lihua JiangAbstract:Mitochondrial genome (mitogenome) structure and gene order are generally considered conserved in vertebrates. However, the flatfish (Pleuronectiformes) mitogenomes exhibit the most diversified gene rearrangement patterns. Here, we report a newly sequenced mitogenome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae). The total length of the C. melampetalus mitogenome is 16,651 bp, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a putative control region, and an L-strand replication origin. Like all previously reported tongue sole (Cynoglossinae) mitogenomes, the C. melampetalus tRNA-Gln gene is inverted from the light to the heavy strand (Q inversion), accompanied by the translocation of CR, which is downstream to the 3'-end of ND1. In addition, we observed a unique tRNA-Ile-Met-Glu (IMQ) gene order that differed from the tRNA-Glu-Ile-Met (QIM) order previously reported for other 14 Cynoglossinae mitogenomes. To our knowledge, it is the first report of two different patterns of mitogenomic gene-arrangement within the same genus in teleost. According to the Q inversion, Met pseudogene (ψMet) and long intergenic gap (186 bp) between M and Q genes, the observed gene rearrangement pattern were presumably supported by mitochondrial recombination and tandem duplication/random loss models. The reduced trend of the intergenic gap between Q and I also suggests that the event of gene rearrangement can be traced back to early Cynoglossinae differentiation.
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the complete mitochondrial genome sequence of cynoglossus roulei Pleuronectiformes cynoglossidae
Mitochondrial DNA Part B, 2019Co-Authors: Shixi Chen, Wei Shi, Hairong Luo, Jiangxing Dong, Xiao-yu KongAbstract:The complete mitogenome of Cynoglossus roulei is 16,598 bp in length, containing 37 genes, among them, ND6 and eight tRNA genes are encoded by L-strand and other genes by H-strand, which are as sam...
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the complete mitochondrial genome sequence of asterorhombus intermedius Pleuronectiformes bothidae
Mitochondrial DNA Part B, 2019Co-Authors: Shixi Chen, Wei Shi, Hairong Luo, Xiao-yu KongAbstract:The complete mitogenome of Asterorhombus intermedius is 16,886 bp in length, containing 37 genes, among them, ND6 and eight tRNA genes are encoded by L-strand, and other genes by H-strand, which ar...
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Remarkable sequence polymorphisms in 18S rDNA of Pleuronichthys cornutus (Pleuronectiformes: Pleuronectidae).
Gene, 2018Co-Authors: Min Yang, Wei Shi, Xiao-yu Kong, Li Gong, Hairong LuoAbstract:Abstract Highly conserved 18S rDNA sequences encode ribosomal RNA and evolve in a concerted manner. In this study, 178 sequences of 18S rDNA from the ridge-eyed flounder, Pleuronichthys cornutus, were analyzed. The total sequences yielded five distinguishable types of 18S rDNA—A, B, R, S, and L—that were defined based on sequence alignments, clone clustering, and recombination detection. The length of 176 clones ranged from 1838 bp to 1846 bp, with one particularly short clone reaching only 1466 bp and one long clone reaching up to1869 bp. As per current criteria for pseudogene inference, Type S was inferred to be a pseudogene due to its truncated length (380 bp) and low minimum free energy (−536.9 kcal·mol−1). Type L had a unique 20-bp insertion and was also predicted to be as a pseudogene. Types A and B showed 31 differential sites, which in Type A was consistent with 18S rDNA sequences found in six other flounders, while Type B and recombinant Type R were not. Maximum K2P genetic distances were calculated within Type B (0.0232) and R (0.0313); these were much higher than that of Type A (0.0093) or between the six flounders (0.011). Only Type A was detected by reverse transcription experiments and linked to functional ITS1 and 5.8S fragments; Types B and R were linked to both functional and pseudo genes. Accordingly, Type A is likely the functional gene, and Types B and R are probable pseudogenes. The heterogeneity of the five types revealed that 18S rDNA sequences evolved in a non-concerted evolution manner in P. cornutus. Furthermore, our results suggest that more features should be used to identify functional or pseudo genes.
Li Gong - One of the best experts on this subject based on the ideXlab platform.
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variations in the conserved 18s and 5 8s reveal the putative pseudogenes in 18s its1 5 8s rdna of cynoglossus melampetalus Pleuronectiformes cynoglossidae
Biochemical and Biophysical Research Communications, 2021Co-Authors: Wei Shi, Min Yang, Li Gong, Hairong LuoAbstract:Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.
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novel gene rearrangement pattern in cynoglossus melampetalus mitochondrial genome new gene order in genus cynoglossus Pleuronectiformes cynoglossidae
International Journal of Biological Macromolecules, 2020Co-Authors: Li Gong, Wei Shi, Hairong Luo, Ying Zhang, Liqin Liu, Bingjian Liu, Lihua JiangAbstract:Mitochondrial genome (mitogenome) structure and gene order are generally considered conserved in vertebrates. However, the flatfish (Pleuronectiformes) mitogenomes exhibit the most diversified gene rearrangement patterns. Here, we report a newly sequenced mitogenome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae). The total length of the C. melampetalus mitogenome is 16,651 bp, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a putative control region, and an L-strand replication origin. Like all previously reported tongue sole (Cynoglossinae) mitogenomes, the C. melampetalus tRNA-Gln gene is inverted from the light to the heavy strand (Q inversion), accompanied by the translocation of CR, which is downstream to the 3'-end of ND1. In addition, we observed a unique tRNA-Ile-Met-Glu (IMQ) gene order that differed from the tRNA-Glu-Ile-Met (QIM) order previously reported for other 14 Cynoglossinae mitogenomes. To our knowledge, it is the first report of two different patterns of mitogenomic gene-arrangement within the same genus in teleost. According to the Q inversion, Met pseudogene (ψMet) and long intergenic gap (186 bp) between M and Q genes, the observed gene rearrangement pattern were presumably supported by mitochondrial recombination and tandem duplication/random loss models. The reduced trend of the intergenic gap between Q and I also suggests that the event of gene rearrangement can be traced back to early Cynoglossinae differentiation.
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Remarkable sequence polymorphisms in 18S rDNA of Pleuronichthys cornutus (Pleuronectiformes: Pleuronectidae).
Gene, 2018Co-Authors: Min Yang, Wei Shi, Xiao-yu Kong, Li Gong, Hairong LuoAbstract:Abstract Highly conserved 18S rDNA sequences encode ribosomal RNA and evolve in a concerted manner. In this study, 178 sequences of 18S rDNA from the ridge-eyed flounder, Pleuronichthys cornutus, were analyzed. The total sequences yielded five distinguishable types of 18S rDNA—A, B, R, S, and L—that were defined based on sequence alignments, clone clustering, and recombination detection. The length of 176 clones ranged from 1838 bp to 1846 bp, with one particularly short clone reaching only 1466 bp and one long clone reaching up to1869 bp. As per current criteria for pseudogene inference, Type S was inferred to be a pseudogene due to its truncated length (380 bp) and low minimum free energy (−536.9 kcal·mol−1). Type L had a unique 20-bp insertion and was also predicted to be as a pseudogene. Types A and B showed 31 differential sites, which in Type A was consistent with 18S rDNA sequences found in six other flounders, while Type B and recombinant Type R were not. Maximum K2P genetic distances were calculated within Type B (0.0232) and R (0.0313); these were much higher than that of Type A (0.0093) or between the six flounders (0.011). Only Type A was detected by reverse transcription experiments and linked to functional ITS1 and 5.8S fragments; Types B and R were linked to both functional and pseudo genes. Accordingly, Type A is likely the functional gene, and Types B and R are probable pseudogenes. The heterogeneity of the five types revealed that 18S rDNA sequences evolved in a non-concerted evolution manner in P. cornutus. Furthermore, our results suggest that more features should be used to identify functional or pseudo genes.
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the complete mitochondrial genome of pseudaesopia japonica Pleuronectiformes soleidae
Mitochondrial DNA, 2017Co-Authors: Li Gong, Wei Shi, Min Yang, Xiao-yu KongAbstract:The Pseudaesopia japonica belongs to family Soleidae in order Pleuronectiformes. In this study, the complete mitochondrial genome of P. japonica was determined and described. The mitogenome is 16 790 bp in length and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs, one control region, and a light strand replication origin. The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 28.5%, 25.7%, 30.3%, and 15.5%, for A, T, C, and G, respectively, with a slight bias on A + T content (54.3%). The maximum likelihood phylogeny tree of 22 flatfishes demonstrated that the species from Zebrias and Aesopia firstly formed a sister group, and then clustered in the same clade with P. japonicas. This study is expected to contributing to the systematic evolution of P. japonicas and further phylogenetic relationship of Soleidae and Pleuronectiformes.
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non concerted evolution in ribosomal its2 sequence in cynoglossus zanzibarensis Pleuronectiformes cynoglossidae
Biochemical Systematics and Ecology, 2016Co-Authors: Li Gong, Wei Shi, Min Yang, Xiao-yu KongAbstract:The nuclear ribosomal RNA genes (nrDNA) include three rRNA genes (18S, 5.8S, and 28S) and two internal transcribed spacers (ITS1 and ITS2). The lack of variability in nrDNA has been explained as the result of concerted evolution. In fact, many examples of variation have been discovered, suggesting a non-concerted evolution process. There are few studies on ITS2 in teleostean fishes; particularly no reports on flatfishes. In this study, we focused on ITS2 in Zanzibar tonguesole, Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae). Three types of ITS2 sequences (Type A, B, and C) coexisted and mainly differ in length, nucleotide diversity (π), secondary structure, and minimum free energy. Based on these different features, Type B and C were speculated as the putative pseudogenic ITS2 region. Moreover, Type C sequences were detected as recombinant from crossing over between Type A and B sequences. To our knowledge, this is the first report on ITS2 recombination in animal ribosomal RNA genes. The high degree of ITS2 sequence polymorphism at the intraindividual level supported a non-concerted evolution pattern in the C. zanzibarensis genome. These results provide useful data for further studies on ITS2 in flatfishes and contribute to polymorphism analyses of ribosomal RNA genes in teleostean fishes.
Paulino Martínez - One of the best experts on this subject based on the ideXlab platform.
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Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production.
Comparative biochemistry and physiology. Part D Genomics & proteomics, 2016Co-Authors: Diego Robledo, Carmen Bouza, Miguel Hermida, Juan A. Rubiolo, Carlos Fernández, Andrés Blanco, Paulino MartínezAbstract:Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
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Phylogenetic analysis of the order Pleuronectiformes (Teleostei) based on sequences of 12S and 16S mitochondrial genes
Genetics and Molecular Biology, 2008Co-Authors: Marisa Fagundes Carvalho De Azevedo, Belén G Pardo, Paulino Martínez, Claudio Oliveira, Fausto ForestiAbstract:The fish order Pleuronectiformes, composed of 14 families, has two suborders: Psettodoidei (with one family) and Pleuronectoidei (with thirteen families). The relationships among families of Pleuronectoidei and among the genera of their families have extensively been debated and a consensus has not yet been reached. In the present study, partial sequences of the 12S and 16S mitochondrial rRNA genes were obtained from 19 species belonging to the families Achiridae, Bothidae, Cynoglossidae, Paralichthyidae, Pleuronectidae, Scophthalmidae, and Soleidae. Additional sequences of 42 pleuronectiform species were obtained from GenBank. Phylogenetic analyses were conducted by the methods of maximum-parsimony, maximum-likelihood and Bayesian inference. Our results corroborate the monophyletic status of all families, excluding Paralichthyidae. In the family Achiridae, the genus Catathyridium (freshwater) was the sister group of Trinectes (saltwater), and Hypoclinemus (freshwater) was the sister group of Achirus (saltwater). Assuming that the putative ancestor of achirids lived in saltwater, it is suggested that the freshwater habitats in South America were colonized independently by different achirid lineages.
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phylogenetic analysis of flatfish order Pleuronectiformes based on mitochondrial 16s rdna sequences
Scientia Marina, 2005Co-Authors: Belén G Pardo, L. Sánchez, Annie Machordom, Fausto Foresti, Fabio Portoforesti, Marisa Fagundes Carvalho De Azevedo, Rafael Banon, Paulino MartínezAbstract:SUMMARY: The phylogenetic relationships of the order Pleuronectiformes are controversial and at some crucial points remain unresolved. To date most phylogenetic studies on this order have been based on morpho-anatomical criteria, whereas only a few sequence comparisons based studies have been reported. In the present study, the phylogenetic relationships of 30 flatfish species pertaining to seven different families were examined by sequence analysis of the first half of the 16S mitochondrial DNA gene. The results obtained did not support percoids as the sister group of pleuronectiforms. The monophyletic origin of most families analyzed, Soleidae, Scophthalmidae, Achiridae, Pleuronectidae and Bothidae, was strongly supported, except for Paralichthyidae which was clearly subdivided into two groups, one of them associated with high confidence to Pleuronectidae. The analysis of the 16S rRNA gene also suggested the monophyly of Pleuronectiforms as the most probable hypothesis and consistently supported some major interfamily groupings.
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Localization of ribosomal genes in Pleuronectiformes using Ag-, CMA_3-banding and in situ hybridization
Heredity, 2001Co-Authors: Belén G Pardo, Carmen Bouza, Jaime Castro, Paulino Martínez, Laura SánchezAbstract:In this paper we present the analysis of nucleolar organizer regions (NORs) in five species of the order Pleuronectiformes ( Scophthalmus maximus, Scophthalmus rhombus, Platichthys flesus, Solea solea and Solea lascaris ), a group of fish poorly studied cytogenetically. In spite of the small chromosome sizes, which characterize the karyotypes of this group, we implement both classical (Ag- and CMA_3-staining) and molecular ( in situ hybridization with a major rDNA probe) techniques for NOR location. NORs were localized in a single chromosome pair in all species studied and showed size variation within each species. Evidence of a NOR-site polymorphism was detected in Platichthys flesus and Scophthalmus maximus . NOR location was apparently the same within families ( S. rhombus vs. S maximus , and S. solea vs. S. lascaris ) but clearly differed among families, and supports the phylogenetic relationships proposed for the order Pleuronectiformes.
Min Yang - One of the best experts on this subject based on the ideXlab platform.
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variations in the conserved 18s and 5 8s reveal the putative pseudogenes in 18s its1 5 8s rdna of cynoglossus melampetalus Pleuronectiformes cynoglossidae
Biochemical and Biophysical Research Communications, 2021Co-Authors: Wei Shi, Min Yang, Li Gong, Hairong LuoAbstract:Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.
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Remarkable sequence polymorphisms in 18S rDNA of Pleuronichthys cornutus (Pleuronectiformes: Pleuronectidae).
Gene, 2018Co-Authors: Min Yang, Wei Shi, Xiao-yu Kong, Li Gong, Hairong LuoAbstract:Abstract Highly conserved 18S rDNA sequences encode ribosomal RNA and evolve in a concerted manner. In this study, 178 sequences of 18S rDNA from the ridge-eyed flounder, Pleuronichthys cornutus, were analyzed. The total sequences yielded five distinguishable types of 18S rDNA—A, B, R, S, and L—that were defined based on sequence alignments, clone clustering, and recombination detection. The length of 176 clones ranged from 1838 bp to 1846 bp, with one particularly short clone reaching only 1466 bp and one long clone reaching up to1869 bp. As per current criteria for pseudogene inference, Type S was inferred to be a pseudogene due to its truncated length (380 bp) and low minimum free energy (−536.9 kcal·mol−1). Type L had a unique 20-bp insertion and was also predicted to be as a pseudogene. Types A and B showed 31 differential sites, which in Type A was consistent with 18S rDNA sequences found in six other flounders, while Type B and recombinant Type R were not. Maximum K2P genetic distances were calculated within Type B (0.0232) and R (0.0313); these were much higher than that of Type A (0.0093) or between the six flounders (0.011). Only Type A was detected by reverse transcription experiments and linked to functional ITS1 and 5.8S fragments; Types B and R were linked to both functional and pseudo genes. Accordingly, Type A is likely the functional gene, and Types B and R are probable pseudogenes. The heterogeneity of the five types revealed that 18S rDNA sequences evolved in a non-concerted evolution manner in P. cornutus. Furthermore, our results suggest that more features should be used to identify functional or pseudo genes.
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the complete mitochondrial genome of pseudaesopia japonica Pleuronectiformes soleidae
Mitochondrial DNA, 2017Co-Authors: Li Gong, Wei Shi, Min Yang, Xiao-yu KongAbstract:The Pseudaesopia japonica belongs to family Soleidae in order Pleuronectiformes. In this study, the complete mitochondrial genome of P. japonica was determined and described. The mitogenome is 16 790 bp in length and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs, one control region, and a light strand replication origin. The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 28.5%, 25.7%, 30.3%, and 15.5%, for A, T, C, and G, respectively, with a slight bias on A + T content (54.3%). The maximum likelihood phylogeny tree of 22 flatfishes demonstrated that the species from Zebrias and Aesopia firstly formed a sister group, and then clustered in the same clade with P. japonicas. This study is expected to contributing to the systematic evolution of P. japonicas and further phylogenetic relationship of Soleidae and Pleuronectiformes.
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non concerted evolution in ribosomal its2 sequence in cynoglossus zanzibarensis Pleuronectiformes cynoglossidae
Biochemical Systematics and Ecology, 2016Co-Authors: Li Gong, Wei Shi, Min Yang, Xiao-yu KongAbstract:The nuclear ribosomal RNA genes (nrDNA) include three rRNA genes (18S, 5.8S, and 28S) and two internal transcribed spacers (ITS1 and ITS2). The lack of variability in nrDNA has been explained as the result of concerted evolution. In fact, many examples of variation have been discovered, suggesting a non-concerted evolution process. There are few studies on ITS2 in teleostean fishes; particularly no reports on flatfishes. In this study, we focused on ITS2 in Zanzibar tonguesole, Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae). Three types of ITS2 sequences (Type A, B, and C) coexisted and mainly differ in length, nucleotide diversity (π), secondary structure, and minimum free energy. Based on these different features, Type B and C were speculated as the putative pseudogenic ITS2 region. Moreover, Type C sequences were detected as recombinant from crossing over between Type A and B sequences. To our knowledge, this is the first report on ITS2 recombination in animal ribosomal RNA genes. The high degree of ITS2 sequence polymorphism at the intraindividual level supported a non-concerted evolution pattern in the C. zanzibarensis genome. These results provide useful data for further studies on ITS2 in flatfishes and contribute to polymorphism analyses of ribosomal RNA genes in teleostean fishes.
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the complete mitochondrial genome of cynoglossus puncticeps Pleuronectiformes cynoglossidae
Mitochondrial DNA, 2016Co-Authors: Min Yang, Wei Shi, Xianguang Miao, Xiao-yu KongAbstract:Cynoglossus puncticeps (Soleoidei Cynoglossidae) is characterized by both eyes on the left side of the body. Here we report the mitogenome of this tonguesole for the first time, which is 17,142 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 position between the ND1 and the tRNA-Gln genes, leaving a 25-bp trace fragment in the original location. In addition, two tandem arrays were found: one was a 17-bp motif with 40.2 copies, and the other was 73-bp with 3.0 copies.