Characterization of the complete mitochondrial genome of the medical pipefish Doryichthys boaja Bleeker 1850

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Doryichthys boaja Bleeker 1850 ( long-snouted pipefish ) was a fresh water and estuarine pipefish species that occurred widely in Southeast Asia. It was one of the largest fresh water pipefishes, reaching up to 44 centimeter in distance ( Kuiter 2000 ). Doryichthys boaja was wide distributed in the streams, rivers, and brackish waters of southeast Asia. Since the overexploitation and habitat end, this species is now listed in the IUCN Red List of Threatened Species as Data Deficient. Similar to all early syngnathids, this species was ovoviviparous, and the males brood the embryo under their trunk anterior to giving live parentage ( Wilson et alabama. 2001 ). Since there are morphologic similarities between D. boaja and other Syngnathidae species, molecular studies based on mitochondrial deoxyribonucleic acid markers have proved to be valuable tools for species identification and phylogenetic relationship elucidation within the syndicate. Compared with fond mtDNA sequences, accomplished mitochondrial genome with a large set of genes was by and large considered as a useful tool for phylogenetic psychoanalysis and promote growth of species designation and restoration strategies ( Cheng et alabama. 2013 ; Cheng, Fang, et alabama. 2017 ). thus, it was utilitarian to obtain the complete mitochondrial deoxyribonucleic acid of D. boaja and studying its phylogenetic side in Genus Syngnathidae, facilitating its familial assay, greater management, and conservation. here, we sequenced and characterized the complete mitochondrial genome of D. boaja. The specimen of D. boaja was obtained from chinese materia medica marketplace in Anguo city of Hebei Province and identified based on its morphometric features, such as the six-cornered, with acute trail edges, and a acanthoid process ( Liu et aluminum. 2018 ). The sample of D. boaja ( FY-26 ) was deposited in the collection center of College of Pharmaceutical Science at Zhejiang Chinese Medical University. Samples used in this study were approved by Animal Ethics committee for experiment, granted by Zhejiang Chinese Medical University. sum genomic deoxyribonucleic acid was extracted from the muscle tissue of tail using a Tiangen DNA extract kit ( Tiangen Inc., Beijing, China ), following the manufacturer ’ randomness instructions. The accomplished mtDNA of D. boaja was amplified and sequenced by 14 pairs of primers designed according to the published mitochondrial genome sequences in the genus Hippocampus ( Cheng, Liao et alabama. 2017 ; Chen et alabama. 2017 ). The mitochondrial genome sequence of D. boaja with the annotate genes was deposited in GenBank under the accession number of MH259592. A total of 13 complete mitochondrial genomes in family Syngnathidae were collected and the phylogenetic relationships were deduce utilize maximum-likelihood ( ML ) methods by MEGA 7.0 based on the concatenated supergene consisting of 13 mitochondrial protein-coding genes ( Kumar et aluminum. 2016 ).

The whole mitochondrial genome sequence of D. boaja had a round genome of 16,562 bp, containing 13 protein-coding genes, 2 rRNA genes, 1 command region and 22 transfer rna genes. The contents of A, C, G, and T were 31.10 %, 24.14 %, 14.36 %, and 30.40 %, respectively. AT and GC contents of mitochondrial genome were 61.50 % and 38.50 %, respectively. The protein code and transfer rna genes of the checkup pipefish mitogenome were predicted using ARWEN ( Laslett and Canback 2008 ). The proportion of coding sequences of D. boaja with a sum length of 11,405 bp was 68.86 %, which encoded 3800 amino acids. All protein-coding genes in D. boaja started with a typical ATG codon, except for COX1 that was initiated by a GTG begin codon. For the stop codon, ND1, ATP8, ATP6, ND4L, ND5, and ND6 genes ended with complete TAA, while the early 7 genes terminated with a one base T or TA. Incomplete stop codon was besides found in the mitochondrial genes of many other fish species ( Yu and Kwak 2015 ; Zhu et alabama. 2018 ). The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 941 bp and 1671 bp, respectively. The 22 transfer rna genes varied from 67 to 74 bp in distance. The tRNA-Ser gene contained a dihydrouridine weapon substitute closed circuit and the other 21 transfer rna genes could be folded into the typical clover-leaf secondary coil structure. exchangeable with most vertebral mitochondrial genome, nucleotide overlaps and space gaps were very common in seahorses and pipefishes ( Cheng et aluminum. 2013 ; Ge et aluminum. 2017 ). The control region locating between tRNA-Pro and tRNA-Phe gene was 948 bp in length, ranging from 15,615 to 16,562 bp.

phylogenetic relationships among D. boaja and other 13 species with accomplished mitogenome sequences were constructed using Solenostomus paradoxus as outgroup. As shown in Figure 1, D. boaja clustered together with Microphis brachyurus with high statistical support, suggesting a relative close relationship between the genus Doryichthys and Microphis. The monophyletic group of D. boaja and M. brachyurus appears deoxyadenosine monophosphate sister to the clade of Doryrhamphus japonicus, indicating that these 3 species shared a more recent coarse ancestor than any early Syngnathidae species. Another checkup pipefish Syngnathoides biaculeatus clustered with Phycodurus eques, while the clade of 5 Hippocampus species was placed as a sister relationship to Corythoichthys flavofasciatus. The data of D. boaja enriched the resource of Syngnathidae in taxonomic, population genetic, and evolutionary biological studies. When the mitogenome representing species from each order in Syngnathidae will be available, the relationship between the species in Syngnathidae will be more clear and accomplished.

calculate 1. Neighbour-joining ( NJ ) tree of 14 species complete mitochondrial genome sequence. The phylogenetic relationships of Doryichthys boaja in Syngnathidae using Sloenostomus paradoxus as the outgroup. Number above each lymph node indicates the ML bootstrap defend values generated from 100 replicates .

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