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Morphological characteristics and DNA barcoding of Pampus echinogaster (Basilewsky, 1855)
Yuan LI, Yan ZHANG, Tianxiang GAO, Zhiqiang HAN, Longshan LIN, Xiumei ZHANG
doi: 10.1007/s13131-017-1124-x
The morphological similarities of Pampus fishes have led to considerable confusion in species-level identification, and no accurate information on neotype or DNA barcoding of Pampus echinogaster is available. Two hundred and seven specimens of P. echinogaster were collected from the coastal waters of Dandong, Dongying, Qingdao, Nantong, Zhoushan, Wenzhou, Changle, Taiwan, and Wakayama (Japan), from June 2010 to April 2013. The diagnostic characteristics of P. echinogaster are as follows: dorsal fin VIII-XI-43–51, anal fin V-VIII-43–49, pectoral fin 22–27, caudal fin 19–22, pelvic fin absent; first gill rakers sparse, slender (pointed), 3–4+12–16=15–20; vertebrae 39–41; transverse occipital canal on top of head moderately small, wavy ridges not reaching upper origin of pectoral fin; ventral branch of lateral line canal spare, shorter than dorsal branch of lateral line canal. By combining congener sequences of the cytochrome oxidase I (COI) gene from GenBank, two absolute groups were detected among all specimens, which further indicated that two valid species were present based on genetic differences in amino acid sequences and the distance between the groups. The sequences of Group 1 can be regarded as DNA barcoding of P. echinogaster. The correct morphological redescription and DNA barcoding of P. echinogaster are presented here to provide a guarantee for efficient and accurate studies, a theoretical basis for classification, and enable appropriate fishery management and conservation strategies for the genus Pampus in the future.
key words: morphological characteristics, DNA barcoding, Pampus echinogaster, genetic differentiation, transverse occipital canal
Long duplication of 18S ribosomal DNA in Cynoglossus lineolatus (Pleuronectiformes: Cynoglossidae): novel molecular evidence for unequal crossing over model
Li GONG, Wei SHI, Min YANG, Lizhen SI, Xiaoyu KONG
doi: 10.1007/s13131-016-0957-z
Although 18S rDNA sequence is extremely conservative, the polymorphism still has been found in few species. In the present study, three types (Type A, B and C) of 18S rDNA sequence coexisted inCynoglossus lineolatus genome, suggesting a non-concerted evolution process, rather than a strictly concerted evolution fashion. Based on the differences of sequence variation, GC content, secondary structure and minimum free energy, Types A and B were speculated as the potential pseudogenes. Additionally, a fascinating finding was a 189-bp duplication of 18S rDNA in Type A sequence. To our knowledge, this is the first report on such a long duplication in teleostean ribosomal DNA. Compared with several theories accounting for the formation of tandem repeats, the unequal crossing over model was thought to be the most likely mechanism to generate the 189-bp duplication of 18S rDNA. These results not only provide a novel molecular evidence for the unequal crossing over model, but also benefit for the further study on 18S rDNA in fishes.
key words: nrDNA, Cynoglossus lineolatus, tandem repeat, pseudogene, polymorphism, non-concerted evolution
Fish diversity and molecular taxonomy in the Prydz Bay during the 29th CHINARE
Yuan LI, Liyan ZHANG, Puqing SONG, Ran ZHANG, Liangming WANG, Longshan LIN
doi: 10.1007/s13131-018-1228-y
In 2013, the 29th Chinese National Antarctic Research Expedition (CHINARE) prospected the Prydz Bay on the Antarctic continental shelf, and the Chinese R/V Xuelong icebreaker sampled all of the examined locations. The nature of Antarctic fish diversity in the high-latitude Prydz Bay is virtually unknown, and the accuracy of relevant estimates has not been established. Thus, it is necessary to evaluate this diversity and propose protective measures. In total, ninety-nine specimens were collected from various locations. To overcome uncertainties associated with identifying species based on morphology, DNA barcoding (COI gene) was employed to reconstruct phylogenetic relationships with delimited references from NCBI. Twenty-two species representing six families were unambiguously identified from a neighbor-joining (NJ) tree and barcoding gaps. With the morphological identification, thirteen species were identified correctly, five species were identified correctly at the genus level, and four species were identified at the close sister species level. Notothenioid dominance was not evident in the Prydz Bay, in contrast to other published studies. The low species diversity and catch biomass during this CHINARE were severely constrained by limited fishing methods and localized sites, which led to biased underestimation. Our analyses indicate that DNA barcoding is an effective tool for the identification of fish species in the Prydz Bay. The identification and distribution of Antarctic fish should be an integral component of understanding Antarctic fish biodiversity and biogeography, and large-scale studies are necessary for the further taxonomic identification of Antarctic fish.
key words: DNA barcoding, Prydz Bay, Antarctic fish, phylogenetic relationship, barcoding gap
Development of a 16S rRNA gene-based microarray for the detection of marine bacterioplankton community
Wei ZHAO, Jingjing WANG, Yajie LIANG, Zhiyong HUANG
doi: 10.1007/s13131-017-1055-6
A better understanding of bacterioplankton community shifts following change in marine environments is critical to predict the marine ecosystem function. In order to get a snapshot of the microbial taxonomy profiling of a wide range marine area, a quick, convenient and low cost method would be favorable. In this study, we developed a 16S rRNA gene-based microarray using ARB software, which contained 447 probes targeting 160 families of marine bacteria. The specificity, sensitivity and quantitative capability of this microarray were assessed by single cloned 16S rRNA genes. The reliability of this microarray was tested by eight environmental samples. The results showed that the microarray was specific, only 1.16% false results were detected in five single-clone hybridization tests. The microarray could detect DNA samples as few as 1 ng/μL and the signal intensity could reflect the relative abundance of the bacteria in the range of 1 ng/μL to 100 ng/μL of DNA concentration. Hybridization with environmental samples showed that it can discriminate bacterioplankton communities by sites and time. High throughput sequencing results from the eight samples confirmed the hybridization results. It indicated that this developed microarray could be used as a convenient tool to monitor the bacterioplankton community in marine environment.
key words: microarray, bacterioplankton community, 16S rRNA gene, marine environment
The genus Chiropsoides (Chirodropida: Chiropsalmidae) from the Andaman Sea, Thai waters
doi: 10.1007/s13131-018-1311-4
Box jellyfish Chiropsoides buitendijki from the coastal zone along the Andaman Sea, southwestern Thailand are characterized by a box-shaped body with unilateral branched tentacles and lack of interradial furrows. Tentacular banding was first reported in the present study with 1–3–2–3–2–3–2–3–1 patterns (1–major band, 2–thicker minor band and 3–thinner minor band). The DNA sequences of 18 S ribosomal RNA genes indicated that the specimen examined were genetically similar toC. buitendijki that was previously identified from the Nam Bor Bay, Phuket, Thailand, and distinct to the other known taxa in the order Chirodropida. In addition, a significant genetic divergence based on 16S mitochondrial gene was observed within the C. buitendijki samples. This indicates a population genetic differentiation but needs further confirmation.
key words: Chiropsoides, Cubozoa, Andaman Sea, jellyfish, tentacular banding
Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus)
Yanyan Feng, Dening Zhang, Jianjian Lv, Baoquan Gao, Jian Li, Ping Liu
doi: 10.1007/s13131-019-1428-0
Water salinity condition is an important factor for artificial propagation of the swimming crab (Portunus trituberculatus). Low salinity (LS)-resistant strains are preferred by crab industries. Single nucleotide polymorphism (SNP), the third generation of molecular markers, can be utilized in the breeding of LS-resistant species of P. trituberculatus. Our earlier study identified 615 genes differentially expressed in low-salinity stress compared to the controls. Although thousands of SNP loci have been found, it is hard to identify a SNP marker in correlation with a desired trait. In this study, time-of-flight mass spectrometry (TOF-MS), as an efficient method to select SNPs for the tolerance of LS challenge, was utilized for SNP typing. Fifty gene segments were amplified based on comparative transcriptomics in our earlier study, a total of 18 511 bp DNA fragments were amplified, and eighty-five SNP markers were found. The frequency of the SNPs was estimated to be 0.46 per 100 base pairs of DNA sequences. The rate of the conversion mutation was 81%, while the transversion mutation was 19%. The mutation rate of the G/T (C/A), A/T and G/C was 26%, 12% and 7%, respectively. Eight SNP markers were found to significantly correlate with the adaption of low salinity. Of the eight SNP markers, three linked-SNPs were found in the cuticle proportion gene, and another three SNPs were found in three new genes, and the rest two were found in aquaporin gene and chloride channel gene. The development of these SNP markers found in our study could be primarily used for breeding LS-resistant strains of P. trituberculatus.
key words: Portunus trituberculatus, low salinity, time-of-flight mass spectrometry, single nucleotide polymorphism, SNP
Identification and molecular characterization of Cathepsin L gene and its expression analysis during early ontogenetic development of kuruma shrimp Marsupenaeus japonicus
Ying QIAO, Jun WANG, Yong MAO, Min LIU, Xiaohong SONG, Yongquan SU, Chunzhong WANG, Zhipeng ZHENG
doi: 10.1007/s13131-017-0983-5
Cathepsin L gene is a member of the cysteine proteinase gene group. In this study Cathepsin L gene was isolated from Kuruma shrimp Marsupenaeus japonicus (Mj-Cathepsin L) and the full-length DNA sequence was 1 963 bp. Mj-Cathepsin L protein showed high homologies with other Cathepsin L proteins documented in vertebrates, mollusks and other crustaceans. Expression analysis of Mj-Cathepsin L gene in different tissues revealed that it was predominant in hepatopancreas. During early ontogenetic development stages Mj-Cathepsin L showed a development-regulated expression, and the Mj-Cathepsin L showed a molting stage-regulated expression during the five molting stages, inferring its role in the ontogenic development of M. japonicus. Two kinds of forms of Mj-Cathepsin L protein: pro-Cathepsin L and Cathepsin L were measured in hepatopancreas, stomach and intestine by Western Blotting.
key words: Cathepsin L gene, larval development, molting cycle, tissue distribution, Marsupenaeus japonicus

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