Dunxue Chen

Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences

The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585 bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.

Analysis of the variable sites and phylogenetic studies of complete mitochondrial DNA based on the Siniperca scherzeri (Perciformes: Sinipercidae) from four different areas

In this study, we cloned and sequenced the complete mitochondrial DNAs of Chinese mandarin fish, Siniperca scherzeri populations from four different areas of the Yangtze River and the Pearl River systems in China. In the Yangtze River system, fish samples were taken from three regions, Dongting Lake (DT), Poyang Lake (PL) and Xiangjiang River (XR). In the Pearl River system, fish samples were collected from the Lijiang River (LR). The sizes of their complete mitochondrial genome were 16,502 bp (LR), 16,508 bp (PL), 16,502 bp (XR) and 16,508 bp (DT), respectively. The organization of the S. scherzeri mitochondrial genomes was similar to those reported from other fish mitochondrial genomes. Phylogenetic analyses using N–J computational algorithms showed that the Sinipercidaes are monophyletic and can be divided into two genera, Siniperca and Coreoperca. The S. scherzeri could be divided into two groups along the Yangtze River system and the Pearl River.

Complete mitochondrial genome of the blind cave barbel Sinocyclocheilus furcodorsalis (Cypriniformes: Cyprinidae)

Sinocyclocheilus furcodorsalis, a typical cavefish, has evolved some striking characters, for example loss of its eyes and reduction in melanin pigmentation, and can serve as a good model system in evolutionary adaptation developmental mechanisms. So we cloned the complete mitochondrial DNA of S. furcodorsalis (16,581 bp), which is similar to those reported from other fish mitochondrial genomes, containing 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major noncoding control region. The complete mitogenome of the S. furcodorsalis provides an additional important data-set for the study in evolutionary adaptation developmental mechanisms.

Characterization and ontogenetic expression analysis of the myosin light chains from the fast white muscle of mandarin fish Siniperca chuatsi.

Three full-length complementary DNA (cDNA) clones were isolated encoding the skeletal myosin light chain 1 (MLC1; 1237 bp), myosin light chain 2 (MLC2; 1206 bp) and myosin light chain 3 (MLC3; 1079 bp) from the fast white muscle cDNA library of mandarin fish Siniperca chuatsi. The sequence analysis indicated that MLC1 and MLC3 were not produced from differentially spliced messenger RNAs (mRNA) as reported in birds and rodents but were encoded by different genes. The MLC2 encodes 170 amino acids, which include four EF-hand (helix-loop-helix) structures. The primary structures of the Ca(2+)-binding domain were well conserved among the MLC2s of seven other fish species. The ontogenetic expression analysis by real-time PCR showed that the three light-chain mRNAs were first detected in the gastrula stage, and their expression increased from the tail bud stage to the larval stage. All three MLC mRNAs showed longitudinal expression variation in the fast white muscle of S. chuatsi, especially MLC1 which was highly expressed at the posterior area. Taken together, the study provides a better understanding about the MLC gene structure and their expression pattern in muscle development of S. chuatsi.

Selection of Reference Genes for MicroRNA Quantitative Expression Analysis in Chinese Perch, Siniperca chuatsi

Real-time quantitative reverse transcription PCR (RT-qPCR) is one of the most effective and sensitive techniques in gene expression assay, for which selection of reference genes is a prerequisite. In teleost species, such as Chinese perch, the expression profiling of miRNAs as reference genes for RT-qPCR has not been intensively studied. In the present study, the expression profiles of six miRNAs (miR-101a, miR-146a, miR-22a, miR-23a, miR-26a and let-7a) and one small nuclear RNA (U6) were assayed with RT-qPCR in different adult tissues, developmental stages and growth conditions of Chinese perch, Siniperca chuatsi. The analyses revealed that embryonic developmental stage is an important variability factor in the expression stability of miRNAs. All six miRNAs exhibited better expression consistency than U6 in most of the conditions examined, and therefore, they may be more suitable as a reference gene for miRNA quantification. When different tissues and developmental stages were considered, miR-22a demonstrated the most consistent expression pattern, and the best combination of reference genes was miR-22a and miR-23a. Our study offers useful data for selecting miRNAs as reference genes for RT-qPCR analysis of miRNAs in teleost fishes under different conditions.

Molecular characterization and expression regulation of Smyd1a and Smyd1b in skeletal muscle of Chinese perch (Siniperca chuatsi).

Smyd1 is a SET and MYND domain-containing protein, which functions as a histone methyltransferase for control of gene expression and regulates the skeletal and cardiac muscle differentiation. In this study, the full-length cDNA sequences of Smyd1a and Smyd1b were cloned from Chinese perch, and their molecular structure and expression profile in response to nutrition supply and in vivo IGF treatments were also analyzed. The cDNA sequence of Smyd1a and Smyd1b consists of 1862 and 1802 base pairs (bp), encoding 479 and 476 amino acids, respectively. The SET domains of the two proteins were split into two segments by the MYND domain. Furthermore, the amino acid sequence of Smyd1a contains an extra 13-aa insertion in the SET domain in comparison with Smyd1b. The two genes apparently exhibited temporal and spatial differential expression status. In adults, the two genes showed the higher expression level in the muscle and heart than in other testing tissues. During the post-embryonic developmental stages, the higher expression of Smyd1a was detected at 150 days post-hatching (dph), whereas the expression of Smyd1b peaked at 50 dph. It was indicated that they have potential function in muscle developmental regulation. The mRNA levels of Smyd1a and Smyd1b were sharply up-regulated within one day after refeeding in the Chinese perch juveniles following fasting for a week. Moreover, IGF-1 treatments in vivo significantly stimulated their expression in the skeletal muscle. Together, these data provide us with further understanding of the molecular characterization and expression regulation of the two genes upon internal and external stimuli.

Complete mitochondrial genome of the hybrid of Ctenopharyngodon idellus (♀) × Elopichthys bambusa (♂).

Abstract In this study, we determined the complete mitochondrial DNA sequence of the hybrid of Ctenopharyngodon idellus (♀) × Elopichthys bambusa (♂). The total length of the mitochondrial genome was 16,609 bp (accession number KM401549), with the base composition of 31.89% A, 26.33% C, 15.68% G, 26.11% T. The genome contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). Except for ND6 and 8 tRNAs, all other genes were encoded on the heavy strand. The arrangements of these genes were similar to that found in the other teleosts. The complete mitogenome may provide important date set for the study of genetic mechanism in the hybrid fish of Cyprinidae.

The phylogenetic placement of Siniperca obscura base on complete mitochondrial DNA sequence

Abstract The extant freshwater sinipercids represent a group of 12 species and they are endemic to East Asia. In this study, we cloned and sequenced the complete mitochondrial DNA of Siniperca obscura from the Lijiang River. The size of the complete mitochondrial genome is 16,492 bp. The organization of the mitochondrial contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region as well as those reported sinipercid fishes. Among the 13 protein-coding genes, three reading-frame overlaps were found: ATP8 and ATP6 overlap by 10 nucleotides and ND4 and ND4L overlap by 7 nucleotides and ND5 and ND6 overlap by 5 nucleotides. Phylogenetic analyses using N-J and maximum parsimony (MP) computational algorithms showed that S. chuatsi and S. kneri are sister species, next joined by S. Obscura, based on combined 12 protein-coding genes (excluding DN6).

The complete mitochondrial genome sequence of Cirrhinus mrigala (♀) × Labeo rohita (♂)

Abstract We cloned and sequenced the complete mitochondrial DNA (mtDNA) of Cirrhinus mrigala (♀) × Labeo rohita (♂) by PCR-based method. The total of the mtDNA was 16,595 bp. It consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and one putative control region (D-loop region). The overall base composition on strand was as follows A: 32.09%, G: 15.51%, C: 27.95%, T: 24.45%, and the A + T content 56.54%. All the protein-coding genes initiated by typical ATG codon, and ten genes ended with the complete stop codon TAA or TAG, while COII2, ND4 and Cytb genes terminated with GCC, TAT and GCT. The control region contains a thiolases active site, EGF-like domain signature and two anaphylatoxin domain signature. This mitogenome sequence data would play an important role in population genetics and phylogenetics of the hybrid fish in the Cyprinidae family.

Complete mitochondrial genome sequence of Procypris merus.

Abstract In this study, the complete mitochondrianl genome of Procypris merus was sequenced. It was determined to be 16,581 bp and included 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop). The descending order of the base composition on heavy strand was 31.91% A, 24.95% T, 27.39% C, 15.75% G, which is similar to other cyprinid fish mitochondrial genomes. All protein-coding genes had ATG as the start codon but the stop codons have three types. Night genes end with TAA or TAG, and COII, ND4, ND6 and Cytb genes terminate with an incomplete – –T. The complete mitochondrial genome may provide important DNA molecular data for further phylogenetic analyses for higher taxa of Cyprinidae.