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| 1 | A Rapid Analysis Tool for Aerodynamics/Aerothermodynamics of Hypersonic Vehicles显示文摘A rapid engineering surface panel method to analyze aerodynamics and aerothermodynamics of hypersonic vehicles is developed.To obtain the surface pressure distribution of a hypersonic vehicle,the local surface inclination method is applied to calculate the pressure coefficient for each surface panel element,of which the normal vector is corrected first by using an efficient data structure and Rey-casting algorithm,local Reynolds numbers are calculated according to the geometric streamline method,then the aerodynamic heating flux is computed by both reference enthalpy relations and Reynolds analogy method.Several typical test cases are performed and the results indicate that,the developed tool is effective in predicting the aerodynamics/aerothermodynamics for complex geometry of hypersonic vehicle in a wide range of Mach numbers with a sufficient accuracy. | Li Zhengzhou Xiao Tianhang Lü Fanxi Yu Xiongqing Zhang Zhenming Du Sha | 2017 | Transactions of Nanjing University of Aeronautics and Astronautics2017，34，4： | 7 |
| 2 | Two complete mitogenomes of Ocypodoidea(Decapoda: Brachyura), Cleistostoma dilatatum(Camptandriidae) and Euplax sp.(Macrophthalmidae) and its phylogenetic implications显示文摘Complete mitochondrial genomes(mitogenomes) can provide useful information for phylogenetic relationships,gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoidea(Cleistostoma dilatatum and Euplax sp.) were reported for the first time, which are 15 444 bp and16 129 bp in length, respectively. Cleistostoma dilatatum is the first species in the family Camptandriidae whose complete mitogenome was sequenced. Each mitogenome contains an entire set of 37 genes and a putative control region, but their gene arrangements are largely different. Tandem duplication and random loss model is proposed to account for their gene arrangements. Comparative genomic analyses of 19 mitogenomes clustering in one branch reveal that 18 of them shared the same gene rearrangement, while that of C. dilatatum mitogenome was consistent with the ancestral gene arrangement of Brachyura. The dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. Phylogenetic analyses show that all Macrophalmidae species cluster together as a group, and then form a sister clade with Camptandriidae. Moreover, the polyphyly of three superfamilies(Ocypodoidea, Eriphioidea, and Grapsoidea) is reconfirmed. These findings help to confirm the phylogenetic position of Camptandriidae, as well as provide new insights into the phylogeny of Brachyura. | Ying Zhang Liming Wei Bingjian Liu Liqin Liu Zhenming Lü Li Gong | 2023 | Acta Oceanologica Sinica2023，42，4： | 0 |
| 3 | Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications显示文摘Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular evolution.Currently,the phylogenetic location of the genus Varuna(Brachyura:Varunidae)has not been well resolved mainly because of limited representatives(only two extant species).Here,we determined a new mitogenome of this genus(Varuna litterata)and added the published mitogenomes to reconstruct the phylogeny of Varunidae.The 16368-bp mitogenome contains the entire set of 37 genes and a putative control region.The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes.All 16 analyzed mitogenomes have identical gene order and similar molecular features.The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity,with comparatively low variability of COI and COII,and high variability of ND6.The nonsynonymous/synonymous substitution rates(dN/dS ratio)analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure.Twelve tRNA genes,two rRNAs,one PCG,and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order.Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes.Phylogenetic analyses show that all Varunidae species are placed into one group,and form a sister clade with Macrophthalmidae.Nevertheless,the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study.These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes,as well as provide insights into the phylogenetic studies of Brachyura. | Ying Zhang Li Gong Xinting Lu Zengliang Miao Lihua Jiang Bingjian Liu Liqin Liu Pengfei Li Xu Zhang Zhenming Lü | 2022 | Acta Oceanologica Sinica2022，41，6： | 2 |
| 4 | Complete Mitochondrial Genome of Myra affinis(Decapoda:Brachyura:Leucosiidae)and Its Phylogenetic Implications for Brachyura显示文摘Knowledge of complete mitochondrial genomes(mitogenomes)can help understand the molecular evolution and phylogenetic relationships of various species.To date,the phylogenetic status of Leucosiidae within Brachyura remains unresolved because of the limited number of mitogenomes available.In the present study,the complete mitogenome of Myra affinis was sequenced using next-generation sequencing to supplement the limited mitogenome information of Leucosiidae.The 15349 bp-long mitogenome includes 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),2 ribosomal RNAs(rRNAs),and a putative control region.The overall base composition is 34.5%A,36.1%T,11.5%G,and 17.9%C,with a high AT bias(70.6%).All 13 PCGs start with the standard ATN codon and stop with the TAN codon or incomplete T.Except for tRNA-Ser,all other tRNAs have a typical cloverleaf-like secondary structure.Phylogenetic analyses based on the maximum likelihood and Bayesian inference methods are employed to generate identical phylogenetic topologies,thereby supporting the sister relationship between Leucosiidae and Matutidae for the first time.The monophyly of Eubrachyura is well established,and its sister relationship with Raninoida is strongly supported.The results of this work will not only help achieve a better understanding of the characteristics of the M.affinis mitogenome and the phylogenetic position of Leucosiidae,but also provide relevant information for further studies on the phylogeny of Brachyura. | ZHANG Ying MENG Lei MIAO Zengliang WEI Liming LIU Bingjian LIU Liqin GONG Li LÜZhenming | 2022 | Journal of Ocean University of China2022，21，4： | 1 |
| 5 | Comparative mitochondrial genome analysis of Sesarmidae and its phylogenetic implications显示文摘Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first time.The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae species.The 15646-bp mitogenome contains 13 protein-coding genes(PCGs),two ribosomal RNA genes(r RNAs),22 transfer RNA genes(t RNAs),and an A-T rich region.All of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete T.The pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection,whereas the ATP8 gene is an outlier,with pairwise comparison values ranging from neutral selection(0.000)to positive selection(1.039).The gene arrangement of P.eumolpe compared with ancestral Decapoda shows the translocation of two t RNAs(t RNA-His and t RNA-Gln),which is identical to other Sesarmidae species.Phylogenetic analyses show that all Sesarmidae species are placed into one group,and the polyphyly of Eriphioidea,Ocypodoidea,and Grapsoidea is well supported.The relationship between gaps in the QIM region and the phylogeny of Sesarmidae is analyzed.It is obvious that both the G5(the gap between Q and I)and G6(the gap between I and M)decrease progressively with the evolution process.These results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura. | Ying Zhang Lei Meng Liming Wei Bingjian Liu Liqin Liu Zhenming Lü Yang Gao Li Gong | 2022 | Acta Oceanologica Sinica2022，41，8： | 1 |
| 6 | Complete Mitochondrial Genome Analysis of Daphniopsis tibetana(Branchiopoda:Diplostraca):New Insights into the Taxonomy of the Genus and Its Phylogenetic Implications for Branchiopoda显示文摘Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt lakes.D.tibetana can adapt to saline waters,whereas the other species of the superorder Cladocera can only inhabit in freshwater.However,the phylogenetic status of D.tibetana in Branchiopoda remains unclear primarily because of limited mitogenome.In this study,complete mitochondrial genome sequences of D.tibetana were sequenced and annotated for the first time to obtain a comprehensive understanding of its phylogenetic status.The complete mitogenome of D.tibetana is 16196 bp in length.It contains 37 genes,including two ribosomal RNAs(12S and 16S rRNAs)genes,22 transfer RNA(tRNA)genes,13 protein-coding genes,and one non-coding region.The overall base composition is 29.6%A,33.2%T,19.0%G,and 18.2%C with a high AT bias(62.8%).Except for trnS1(GCT),most tRNAs have a typical cloverleaf secondary structure.Phylogenetic analysis based on maximum likelihood and Bayesian inference generates identical phylogenetic topology and shows the phylogenetic status of D.tibetana,which reconfirm the distinction between the genera Daphniopsis and Daphnia.Meanwhile,the class Branchiopoda is clustered into three clades(Anostraca,Notostraca,and Diplostraca)with high support values.These results provide not only a comprehensive understanding of the characteristics of D.tibetana mitogenome and its phylogenetic position in Diplostraca,but also information for future research on the phylogeny of Branchiopoda. | LIU Bingjian PENG Ying LIU Yifan LI Jiasheng ZHANG Kun CHEN Jian GONG Li LIU Liqin LÜZhenming ZHANG Chi | 2022 | Journal of Ocean University of China2022，21，6： | 0 |
| 7 | Comparative mitochondrial genome analysis of Cynoglossidae(Teleost:Pleuronectiformes)and phylogenetic implications显示文摘Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae species.So far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy.Here,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were compared.The length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity.Like most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the L-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in C.puncticpes mitogenome.The typical IQM order(tRNA-Ile-Gln-Met)changed to QIM order.Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C.puncticpes mitogenome.Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future. | Bilin Hu Tingqi Jiang Liming Wei Nannan Zhang Kaixin Wang Liqin Liu Bingjian Liu Jing Liu Zhenming Lü Li Gong | 2023 | Acta Oceanologica Sinica2023，42，11： | 0 |
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