The complete mitochondrial genome of Glyphocrangon regalis (Caridea, Glyphocrangonidae) and the phylogenetic relationships of Caridea
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Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, Jiangsu Province, China
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Abstract
In studying the mitochondrial genome (mitogenome) composition and gene sequences of deep-sea organisms, it is of great importance to understand and explore the molecular mechanisms underlying their adaptation to the deep-sea environment. Glyphocrangon regalis belongs to Caridea, Crangonoidea, and is a typical deep-sea shrimp. In this study, the complete mitogenome of G. regalis was obtained using next-generation sequencing technology. The mitochondrial genes were annotated, and their sequence structures were analysed. The complete mitogenome sequence of G. regalis was 15 918 bp in length, with a base composition of A (36.85%), T (36.68%), C (15.53%) and G (9.94%), exhibiting a significant AT bias with an A + T content of 75.53%. G. regalis encoded a total of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs; among them, 14 genes were located on the negative strand, and 23 genes were located on the positive strand, similar to other caridean shrimp mitogenomes. Additionally, a phylogenetic tree was constructed based on the 13 PCGs of the mitogenomes of 95 species from 12 families within Caridea, supporting the monophyly of various families within Caridea and revealing that G. regalis and species of Pandalidae were the most closely related. This study provides insights into the complete mitogenome of G. regalis, elucidating its genomic characteristics and structural functions. It clarifies the evolutionary status of G. regalis and explores the evolutionary patterns of various families within Caridea through phylogenetic tree construction, thereby providing more references for the study of Caridea systematics.
Résumé
Lorsqu’on étudie la composition du génome mitochondrial (mitogénome) et les séquences de gènes des organismes d’eaux profondes, il est important de comprendre et d’explorer les mécanismes moléculaires qui sous-tendent leur adaptation à l’environnement profond. Glyphocrangon regalis est une crevette profonde typique qui appartient aux Caridea Crangonoidea. Dans cette étude, le mitogénome complet de G. regalis a été obtenu en utilisant la technologie de séquençage de nouvelle génération. Les gènes mitochondriaux ont été annotés, et leurs structures de séquence ont été analysées. La séquence complète du mitogénome de G. regalis avait une longueur de 15,918 bp, avec une composition de base de A (36,85%), T (36,68%), C (15,53%) et G (9,94%), présentant un biais AT significatif avec un contenu A+T de 75,53%. G. regalis codait un total de 37 gènes, incluant 13 gènes codant pour des protéines (PCGs), 22 tRNAs et 2 rRNAs ; parmi eux, 14 gènes étaient situés sur le brin négatif, et 23 sur le brin positif, de façon analogue à d’autres mitogénomes de crevettes Caridea. De plus, un arbre phylogénétique a pu être construit sur la base des 13 PCGs des mitogénomes de 95 espèces appartenant à 12 familles de Caridea, soutenant la monophylie de diverses familles de Caridea et révélant que G. regalis et les espèces de Pandalidae étaient les plus proches apparentées. Cette étude fournit de nouvelles connaissances sur le mitogénome complet de G. regalis, en élucidant ses caractéristiques génomiques et ses fonctions structurelles. Elle clarifie le statut évolutif de G. regalis et explore les schémas évolutifs de diverses familles au sein des Caridea par la construction d’un arbre phylogénétique, apportant ainsi des références supplémentaires pour l’étude de la systématique des Caridea.
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-
Aljanabi, S. M. & I. Martinez, 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Research, 25(22): 4692-4693.
-
Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller & D. J. Lipman, 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17): 3389-3402.
-
Bernt, M., A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf & P. F. Stadler, 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2): 313-319.
-
Boore, J. L. & W. M. Brown, 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev., 8(6): 668-674.
-
Bracken, H. D., S. De Grave, A. Toon, D. L. Felder & K. A. Crandall, 2010. Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda). Zoologica Scripta, 39: 198-212.
-
Chak, S. T. C., P. Barden & J. A. Baeza, 2020. The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus. Sci. Rep., 10(1): 7744.
-
Charbonnier, S., D. Audo, A. Garassino & M. Hyžný, 2017. Fossil Crustacea of Lebanon. Mémoires du Muséum National d’Histoire Naturelle, 210: 1-252.
-
Chen, S., Y. Zhou, Y. Chen & J. Gu, 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17): i884-i890.
-
Cossins, A. R. & A. G. Macdonald, 1989. The adaptation of biological membranes to temperature and pressure: Fish from the deep and cold. Journal of Bioenergetics and Biomembranes, 21(1): 115-135.
-
Cronin, T. J., S. Jones & B. J. Antonio, 2022. The complete mitochondrial genome of the spot prawn, Pandalus platyceros Brandt in Von Middendorf, 1851 (Decapoda: Caridea: Pandalidae), assembled from linked-reads sequencing. Journal of Crustacean Biology, 42(1): ruac003. DOI:10.1093/jcbiol/ruac003.
-
Danovaro, R., P. V. R. Snelgrove & P. Tyler, 2014. Challenging the paradigms of deep-sea ecology. Trends in Ecology & Evolution, 29(8): 465-475.
-
Dierckxsens, N., P. Mardulyn & G. Smits, 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45(4): e18.
-
Dong, J. M., 1988. Deep-sea crustaceans in the East China Sea. (Zhejiang Science and Technology Press, Hang Zhou, China).
-
Elmerot, C., U. Arnason, T. Gojobori & A. Janke, 2002. The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships. Gene, 295(2): 163-172.
-
Guo, Y., H. Liu, J. Feng, J. Li, Y. Ye, B. Guo & C. Qu, 2021. Characterization of the complete mitochondrial genomes of two species of Penaeidae (Decapoda: Dendrobranchiata) and the phylogenetic implications for Penaeoidea. Genomics, 113(1): 1054-1063.
-
Han, Q. & X. Li, 2014. Two new species of Glyphocrangon (Decapoda: Caridea: Glyphocrangonidae) from the East China Sea and the Philippines. Zootaxa, 3852(4): 438-444.
-
Haring, E., L. Kruckenhauser, A. Gamauf, M. J. Riesing & W. Pinsker, 2001. The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors. Molecular Biology and Evolution, 18(10): 1892-1904.
-
Hassanin, A., N. Léger & J. Deutsch, 2005. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Systematic Biology, 54(2): 277-298.
-
Holthuis, L. B., 1971. Biological results of the University of Miami Deep-sea Expeditions. 75. The Atlantic shrimps of the deep-sea genus Glyphocrangon A. Milne-Edwards, 1881. Bulletin of Marine Science, 21(1): 267-373.
-
Jin, J. J., W. B. Yu, J. B. Yang, Y. Song, C. W. dePamphilis, T. S. Yi & D. Z. Li, 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol., 21(1): 241.
-
Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. V. Haeseler & L. S. Jermiin, 2017. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6).
-
Komai, T., 2004. Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 Expedition off Java, Indonesia, with description of one new species. Arquivos do Museu Nacional, 1: 31-44.
-
Kumar, S., G. Stecher, M. Li, C. Knyaz & K. Tamura, 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol., 35(6): 1547-1549.
-
Li, C. P., S. De Grave, T. Y. Chan, H. C. Lei & K. H. Chu, 2011. Molecular systematics of caridean shrimps based on five nuclear genes: Implications for superfamily classification. Zoologischer Anzeiger — A Journal of Comparative Zoology, 250(4): 270-279.
-
Miller, A. D., N. P. Murphy, C. P. Burridge & C. M. Austin, 2005. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Marine Biotechnology, 7: 339-349.
-
Minh, B. Q., H. A. Schmidt, O. Chernomor, D. Schrempf, M. D. Woodhams, A. von Haeseler & R. Lanfear, 2020. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37(5): 1530-1534.
-
Nylander, J., 2004. MrModeltest v2. Program distributed by the author. Available online at http://www.abc.se/~nylander/mrmodeltest2/mrmodeltest2.html.
-
Posada, D., 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol., 25(7): 1253-1256.
-
Posada, D. & K. A. Crandall, 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics, 14(9): 817-818.
-
Rambaut, A., 2017. FigTree-version 1.4. 3, a graphical viewer of phylogenetic trees. Computer program distributed by the author. Available online at http://tree.bio.ed.ac.uk/software/figtree.
-
Rambaut, A., A. J. Drummond, D. Xie, G. Baele & M. A. Suchard, 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol., 67(5): 901-904.
-
Ramos, E. K. d. S., L. Freitas & M. F. Nery, 2020. The role of selection in the evolution of marine turtles mitogenomes. Scientific Reports, 10(1): 16953.
-
Ronquist, F., M. Teslenko, P. van der Mark, D. L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M. A. Suchard & J. P. Huelsenbeck, 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol., 61(3): 539-542.
-
Shen, X., X. Li, Z. Sha, B. Yan & Q. Xu, 2012. Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea. Science China. Life Sciences, 55: 591-598.
-
Sun, J., Y. Zhang, T. Xu, Y. Zhang, H. Mu, Y. Zhang, Y. Lan, C. J. Fields, J. H. L. Hui, W. Li, R. Zhang, W. Nong, F. K. M. Cheung, J. W. Qiu & P. Y. Qian, 2017. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nature Ecology & Evolution, 1(5): 0121.
-
Sun, S. E., J. Cheng, S. Sun & Z. Sha, 2020. Complete mitochondrial genomes of two deep-sea pandalid shrimps, Heterocarpus ensifer and Bitias brevis: insights into the phylogenetic position of Pandalidae (Decapoda: Caridea). Journal of Oceanology and Limnology, 38(3): 816-825.
-
Sun, S. E., M. Hui, M. Wang & Z. Sha, 2018. The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp. Comparative Biochemistry and Physiology (Part D, Genomics and Proteomics), 25: 42-52.
-
Sun, S. E., Z. Sha & Y. Wang, 2021. Mitochondrial phylogenomics reveal the origin and adaptive evolution of the deep-sea caridean shrimps (Decapoda: Caridea). Journal of Oceanology and Limnology, 39(5): 1948-1960.
-
Swofford, D. L., 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10. (Sinauer Associates, Sunderland, MA).
-
Thurber, A. R., A. K. Sweetman, B. E. Narayanaswamy, D. O. B. Jones, J. Ingels & R. L. Hansman, 2014. Ecosystem function and services provided by the deep sea. Biogeosciences, 11(14): 3941-3963.
-
Wang, Q., Z. Wang, D. Tang, X. Xu, Y. Tao, C. Ji & Z. Wang, 2019. Characterization and comparison of the mitochondrial genomes from two Alpheidae species and insights into the phylogeny of Caridea. Genomics, 112(1): 65-70.
-
Wang, Y., K. Y. Ma, L. M. Tsang, K. Wakabayashi, T. Y. Chan, S. De Grave & K. H. Chu, 2021. Confirming the systematic position of two enigmatic shrimps, Amphionides and Procarididae (Crustacea: Decapoda). Zoologica Scripta, 50: 812-823.
-
WoRMS, 2024. World Register of Marine Species. Available online at https://www.marinespecies.org/aphia.php?p=taxdetails&id=107014.
-
Xia, X., 2018. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Mol. Biol. Evol., 35(6): 1550-1552.
-
Xing, J. J., 2005. The types of molecular markers and the researchch and applications of molecular markers technoloyy on the aquatic creature. Chinese Journal of Fisheries, 15(1): 61-70.
-
Xu, Y., L. S. Song & X. Z. Li, 2005. The molecular phylogeny of infraorder Caridea based on 16S rDNA sequences. Marine Sciences Qingdao, Chinese Edition, 29(9): 41.
-
Xu, Y., L. S. Song & X. Z. Li, 2005. The molecular phylogeny of infraorder Caridea based on 16SrDNA sequences. Marine Sciences, 29(9): 38-43.
-
Yang, M., D. Dong & X. Li, 2021. The complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep-sea adaptive evolution of Conoidea. Ecol. Evol., 11(12): 7518-7531.
-
Ye, Y. Y., J. Miao, Y. H. Guo, L. Gong & B. Y. Guo, 2021. The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea. Scientific Reports, 11(1): 14446.
-
Zhang, D., F. Gao, I. Jakovlić, H. Zou, J. Zhang, W. X. Li & G. T. Wang, 2020. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resourc., 20(1): 348-355.
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The complete mitochondrial genome of Glyphocrangon regalis (Caridea, Glyphocrangonidae) and the phylogenetic relationships of Caridea
In: CrustaceanaSearch for other papers by Jian Chen in
Current site
Google Scholar
PubMed
Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, Jiangsu Province, China
Search for other papers by Yuman Sun in
Current site
Google Scholar
PubMed
Search for other papers by Jiji Li in
Current site
Google Scholar
PubMed
Search for other papers by Kaida Xu in
Current site
Google Scholar
PubMed
Search for other papers by Yingying Ye in
Current site
Google Scholar
PubMed
Abstract
In studying the mitochondrial genome (mitogenome) composition and gene sequences of deep-sea organisms, it is of great importance to understand and explore the molecular mechanisms underlying their adaptation to the deep-sea environment. Glyphocrangon regalis belongs to Caridea, Crangonoidea, and is a typical deep-sea shrimp. In this study, the complete mitogenome of G. regalis was obtained using next-generation sequencing technology. The mitochondrial genes were annotated, and their sequence structures were analysed. The complete mitogenome sequence of G. regalis was 15 918 bp in length, with a base composition of A (36.85%), T (36.68%), C (15.53%) and G (9.94%), exhibiting a significant AT bias with an A + T content of 75.53%. G. regalis encoded a total of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs; among them, 14 genes were located on the negative strand, and 23 genes were located on the positive strand, similar to other caridean shrimp mitogenomes. Additionally, a phylogenetic tree was constructed based on the 13 PCGs of the mitogenomes of 95 species from 12 families within Caridea, supporting the monophyly of various families within Caridea and revealing that G. regalis and species of Pandalidae were the most closely related. This study provides insights into the complete mitogenome of G. regalis, elucidating its genomic characteristics and structural functions. It clarifies the evolutionary status of G. regalis and explores the evolutionary patterns of various families within Caridea through phylogenetic tree construction, thereby providing more references for the study of Caridea systematics.
Résumé
Lorsqu’on étudie la composition du génome mitochondrial (mitogénome) et les séquences de gènes des organismes d’eaux profondes, il est important de comprendre et d’explorer les mécanismes moléculaires qui sous-tendent leur adaptation à l’environnement profond. Glyphocrangon regalis est une crevette profonde typique qui appartient aux Caridea Crangonoidea. Dans cette étude, le mitogénome complet de G. regalis a été obtenu en utilisant la technologie de séquençage de nouvelle génération. Les gènes mitochondriaux ont été annotés, et leurs structures de séquence ont été analysées. La séquence complète du mitogénome de G. regalis avait une longueur de 15,918 bp, avec une composition de base de A (36,85%), T (36,68%), C (15,53%) et G (9,94%), présentant un biais AT significatif avec un contenu A+T de 75,53%. G. regalis codait un total de 37 gènes, incluant 13 gènes codant pour des protéines (PCGs), 22 tRNAs et 2 rRNAs ; parmi eux, 14 gènes étaient situés sur le brin négatif, et 23 sur le brin positif, de façon analogue à d’autres mitogénomes de crevettes Caridea. De plus, un arbre phylogénétique a pu être construit sur la base des 13 PCGs des mitogénomes de 95 espèces appartenant à 12 familles de Caridea, soutenant la monophylie de diverses familles de Caridea et révélant que G. regalis et les espèces de Pandalidae étaient les plus proches apparentées. Cette étude fournit de nouvelles connaissances sur le mitogénome complet de G. regalis, en élucidant ses caractéristiques génomiques et ses fonctions structurelles. Elle clarifie le statut évolutif de G. regalis et explore les schémas évolutifs de diverses familles au sein des Caridea par la construction d’un arbre phylogénétique, apportant ainsi des références supplémentaires pour l’étude de la systématique des Caridea.
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 147 | 147 | 62 |
| Full Text Views | 6 | 6 | 3 |
| PDF Views & Downloads | 19 | 19 | 7 |
