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Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024; 277:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.
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Affiliation(s)
- N S Jeena
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India.
| | - Summaya Rahuman
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology (CMLRE), Kochi, Kerala, India
| | - Rajan Kumar
- Shellfish Fisheries Division, Regional Station of CMFRI, Veraval, Gujarat, India
| | - K A Sajeela
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Joe K Kizhakudan
- Mariculture Division, Regional Centre of CMFRI, Visakhapatnam, Andhra Pradesh, India
| | | | - Subal Kumar Roul
- Finfish Fisheries Division, Regional Station of CMFRI, Digha, West Bengal, India
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Hettiarachchi SA, Hyeon JY, Mahardini A, Kim HS, Byun JH, Kim HJ, Jeong JG, Yeo JK, Kim SK, Kim SJ, Heo YS, Sathyadith J, Kang DH, Hur SP. DNA barcoding and morphological identification of spiny lobsters in South Korean waters: a new record of Panulirus longipes and Panulirus homarus homarus. PeerJ 2022; 10:e12744. [PMID: 35047236 PMCID: PMC8757375 DOI: 10.7717/peerj.12744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.
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Affiliation(s)
- Sachithra Amarin Hettiarachchi
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Yeon Hyeon
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Angka Mahardini
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea
| | - Hyung-Suk Kim
- Department of Kinesiology, Jeju National University, Jeju, Republic of Korea
| | - Jun-Hwan Byun
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea
| | - Han-Jun Kim
- Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jong-Gyun Jeong
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Jung-Kyu Yeo
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Shin-Kwon Kim
- Aquaculture Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Se-Jae Kim
- Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Youn-Seong Heo
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Jonathan Sathyadith
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Do-Hyung Kang
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Sung-Pyo Hur
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
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Conrad I, Craft A, Thurman CL, Baeza JA. The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes. Genomics 2020; 113:565-572. [PMID: 32980522 DOI: 10.1016/j.ygeno.2020.09.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/10/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Minuca minax is a semi-terrestrial crustacean that commonly lives in low salinity, riverine habitats along the shores of the eastern United States. This study reports, for the first time, the complete mitochondrial genome of M. minax. The AT-rich mitochondrial genome of M. minax is 15,937 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 737 bp long intergenic space is assumed to be the D-loop. Most of the PCGs and tRNA genes are encoded in the L-strand. The gene order observed in the mitochondrial genome of M. minax is new although almost identical to that reported in confamiliar species. In all other confamiliar species to which M. minax is compared, the positions of the trnQ gene and the trnI gene are switched. KA/KS ratios calculated for all mitochondrial PCGs show values of <1, indicating that these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 15 species) supports the monophyly of the subfamilies Ocypodinae and Gelaminidae. Mitochondrial PCGs have enough phylogenetic information to reveal relationships supporting higher taxonomic levels within this family. The knowledge of a complete mitochondrial genome from the red-jointed brackish-water fiddler crab M. minax contributes to the better understanding of meta-population connectivity and the mechanisms involved in the adaptation of marine organisms to near-limnic conditions.
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Affiliation(s)
- Isabelle Conrad
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Abby Craft
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Carl L Thurman
- Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614-0421, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Chak STC, Barden P, Baeza JA. The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus. Sci Rep 2020; 10:7744. [PMID: 32385299 PMCID: PMC7210941 DOI: 10.1038/s41598-020-64269-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/13/2020] [Indexed: 01/10/2023] Open
Abstract
In the marine realm, eusociality is only known to have evolved within a clade of sponge-dwelling snapping shrimps in the genus Synalpheus. Deciphering the genomic underpinnings of eusociality in these marine shrimps has been limited by the sparse genomic resources in this genus. Here, we report, for a eusocial shrimp Synalpheus microneptunus, a complete mitochondrial genome (22X coverage) assembled from short Illumina 150 bp paired-end reads. The 15,603 bp long mitochondrial genome of S. microneptunus is AT-rich and includes 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and an 834 bp intergenic region assumed to be the D-loop. The gene order is identical to that reported for most caridean shrimps and corresponds to the presumed Pancrustacean ground pattern. All PCGs showed signs of purifying selection, with KA/KS <<1 across the whole PCGs and most sliding windows within PCGs. Maximum-likelihood and Bayesian inference phylogenetic analyses of 13 PCGs and 68 terminals supports the monophyly of the Caridea and the family Alpheidae. The complete mitochondrial genome of the eusocial shrimp Synalpheus microneptunus will contribute to a better understanding of the selective pressures and rates of molecular evolution in marine eusocial animals.
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Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Zhao Y, Zhu X, Li Y, Han Z, Xu W, Dong J, Wei H, Li X. Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species. Sci Rep 2019; 9:17301. [PMID: 31754188 PMCID: PMC6872720 DOI: 10.1038/s41598-019-53539-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/07/2019] [Indexed: 01/19/2023] Open
Abstract
The mitogenome of Chinese grass shrimp, Palaemonetes sinensis, was determined through Illumina sequencing, and the basic characteristics and gene arrangement were analyzed. The mitogenome of P. sinensis was 15955 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and one control region, with tightly packed. 33 of these genes were encoded on the heavy strand, and the remainders encoded on the light strand. The composition of P. sinensis mitogenome presented a strong A + T bias, which account for 66.7%. All PCGs were initiated by a canonical ATN codon, except nad5, which was initiated by GTG. The termination codons of the PCGs were TAA, TAG and T-. The secondary structures of 22 tRNAs of P. sinensis had the typical clover structure, except of trnS1 owing to the lack of dihydroxyuridine (DHU) arm. Gene order comparison of P. sinensis and previously-sequenced Palaemoninae revealed a unique translocation between trnT and trnP in Macrobrachium. The phylogenetic analyses showed that three Exopalaemon species formed a monophyletic group and then clustered with two Palaemon species and P. sinensis successively whereas Macrobrachium clustered with Palaemon capensis in the other clade.
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Affiliation(s)
- Yingying Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Xiaochen Zhu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingdong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhibin Han
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Weibin Xu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jing Dong
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hua Wei
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaodong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- Panjin Guanghe Crab Industry Co.Ltd., Panjin, 124000, China
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Li JY, Zeng C, Yan GY, He LS. Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench. Sci Rep 2019; 9:2610. [PMID: 30796230 PMCID: PMC6385184 DOI: 10.1038/s41598-019-38735-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
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Affiliation(s)
- Jun-Yuan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Zeng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- Hunan Agricultural University, Changsha, Hunan, China
| | - Guo-Yong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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Baeza JA. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus. Sci Rep 2018; 8:17690. [PMID: 30523272 PMCID: PMC6283867 DOI: 10.1038/s41598-018-36132-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Panulirus argus is a keystone species and target of the most lucrative fishery in the Caribbean region. This study reports, for the first time, the complete mitochondrial genome of Panulirus argus (average coverage depth nucleotide-1 = 70×) assembled from short Illumina 150 bp PE reads. The AT-rich mitochondrial genome of Panulirus argus was 15 739 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 801 bp long intergenic space was assumed to be the D-loop. Most of the PCGs were encoded on the H-strand. The gene order observed in the mitochondrial genome of Panulirus argus corresponds to the presumed Pancrustacean ground pattern. KA/KS ratios calculated for all mitochondrial PCGs showed values < 1, indicating that all these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 154 arthropods) supported the monophyly of the Achelata and other infraorders within the Decapoda. Mitochondrial PCGs have enough phylogenetic informativeness to explore high-level genealogical relationships in the Pancrustacea. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus will contribute to the better understanding of meta-population connectivity in this keystone overexploited species.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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8
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Xiao BH, Zhang W, Yao W, Liu CW, Liu L. Analysis of the complete mitochondrial genome sequence of Palinura homarus. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:60-61. [PMID: 33490437 PMCID: PMC7800352 DOI: 10.1080/23802359.2017.1280703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The complete mitochondrial genome sequence of Palinura homarus was obtained using PCR amplification and walking sequencing (GenBank accession no. JN_542716). The complete mitochondrial genome of P. homarus was 15,665 bp long and showed significant AT bias (67% AT content, 33% GC content). The A + T-rich region included copy-related control information and a poly (dT) structure that related to replication and transcription. In this study, the gene arrangement was consistent with other Palinura mitochondrial genomes and the sequence was strikingly similar to Panulirus ornatus, which would be useful in species identification and natural resources conservation.
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Affiliation(s)
- Bao-Hua Xiao
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal, College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China
| | - Wuchai Zhang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal, College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Wei Yao
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal, College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Chu-Wu Liu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal, College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Li Liu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal, College of Fisheries, Guangdong Ocean University, Zhanjiang, China
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Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics 2016; 17:1016. [PMID: 28105939 PMCID: PMC5249044 DOI: 10.1186/s12864-016-3357-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal. RESULTS Three complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods. CONCLUSIONS The mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.
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Affiliation(s)
- Elena V. Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Vladimir V. Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Ravil M. Kamaltynov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Kirill V. Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Maria D. Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420012 Russian Federation
| | - Elena A. Sirotinina
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Alexander Yu. Gornov
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Anton S. Anikin
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Dmitry Yu. Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
- Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, 664003 Russian Federation
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Kim G, Yoon TH, Park WG, Park JY, Kang JH, Park H, Kim HW. Complete mitochondrial genome of Australian spiny lobster, Panulirus cygnus (George, 1962) (Crustacea: Decapoda: Palinuridae) from coast of Australia. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4576-4577. [PMID: 26540371 DOI: 10.3109/19401736.2015.1101571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We characterized the total mitochondrial genome of Australian spiny lobster, Panulirus cygnus (George, 1962), which is found along the western coast of Australia. Total mitochondrial genome length of P. cygnus was 15 724 bp, in which 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs, and a putative control region were encoded. Nine and four protein-coding genes are encoded on the H-strand and on the L-strand, respectively. According to the phylogenetic analysis, P. cygnus was most closely related to Panulirus japonicus among the compared six species belonging to Palinuridae. Although overall gene organization was the same, the putative control region (between SrRNA gene and tRNAIlel) is least similar to one another among mitochondrial genomes from the compared six species belonging to Palinuridae.
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Affiliation(s)
- Gyungryul Kim
- a Interdisciplinary Program of Biomedical Engineering, Pukyong National University , Busan , South Korea
| | - Tae-Ho Yoon
- a Interdisciplinary Program of Biomedical Engineering, Pukyong National University , Busan , South Korea
| | - Won Gyu Park
- b Department of Marine Biology , Pukyong National University , Busan , Korea
| | - Jung Youn Park
- c Fisheries Resources Research Division, National Fisheries Research and Development Institute , Busan , Republic of Korea , and
| | - Jung-Ha Kang
- c Fisheries Resources Research Division, National Fisheries Research and Development Institute , Busan , Republic of Korea , and
| | - Hyun Park
- d Korea Polar Research Institute, Korea Ocean Research and Development Institute , Incheon , South Korea
| | - Hyun Woo Kim
- a Interdisciplinary Program of Biomedical Engineering, Pukyong National University , Busan , South Korea.,b Department of Marine Biology , Pukyong National University , Busan , Korea
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MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Mol Phylogenet Evol 2015; 85:180-8. [DOI: 10.1016/j.ympev.2015.02.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/20/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
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Ahn DH, Kim S, Park JK, Shin S, Min GS. The complete mitochondrial genome of the Japanese fan lobster Ibacus ciliatus (Crustacea, Achelata, Scyllaridae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1871-3. [PMID: 25329294 DOI: 10.3109/19401736.2014.971265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Slipper lobsters are a unique group of decapod crustaceans; they have cylindrical or flattened bodies and belong to the family Scyllaridae. The genus Ibacus (Leach, 1815) (Achelata, Scyllaridae, Ibacinae) consists of eight recognized species to date, all of which occur in the Indo-West Pacific Ocean and are commercially important seafood species. The complete mitochondrial genome of the Japanese fan lobster Ibacus ciliatus (Von Siebold, 1824) is 15,696 bp in size and consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 783 bp. The base composition of I. ciliatus is 35.8% A, 34.7% T, 19.0% C, and 10.5% G, with an overall AT content of 70.5%. The mitogenome of I. ciliatus was found to have gene arrangement and transcriptional polarity identical to that of the American lobster Homarus americanus, showing the pancrustacean ground pattern. Here, we present the complete mitogenome sequence of I. ciliatus; it is the first mitogenome information from the subfamily Ibacinae, and represents the second for the family Scyllaridae.
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Affiliation(s)
- Dong-Ha Ahn
- a Department of Biological Sciences , Inha University , Incheon , South Korea
| | - Sanghee Kim
- b Division of Life Sciences , Korea Polar Research Institute, KIOST , Incheon , South Korea
| | - Joong-Ki Park
- c Department of Parasitology , College of Medicine, Chungbuk National University , Cheongju , South Korea , and
| | - Sook Shin
- d Department of Life Science , Sahmyook University , Seoul , South Korea
| | - Gi-Sik Min
- a Department of Biological Sciences , Inha University , Incheon , South Korea
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Gan HM, Tan MH, Eprilurahman R, Austin CM. The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:337-8. [PMID: 24617471 DOI: 10.3109/19401736.2014.892105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of a highland freshwater crayfish, Cherax monticola, was recovered by shotgun sequencing. The mitogenome consists of 15,917 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of C. monticola is 33.46% for T, 21.48% for C, 33.71% for A and 11.35% for G, with an AT bias of 67.17%.
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Affiliation(s)
- Han Ming Gan
- a School of Science, Monash University Malaysia , Selangor , Malaysia and
| | - Mun Hua Tan
- a School of Science, Monash University Malaysia , Selangor , Malaysia and
| | - Rury Eprilurahman
- b Faculty of Biology , Universitas Gadjah Mada , Yogyakarta , Indonesia
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Gan HM, Schultz MB, Austin CM. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 2014; 14:19. [PMID: 24484414 PMCID: PMC3915555 DOI: 10.1186/1471-2148-14-19] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/29/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. RESULTS The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. CONCLUSIONS We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.
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Affiliation(s)
- Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia.
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Yang CH, Liu Y, Cui Z, Chan TY. Complete mitochondrial genome of the furry lobsterPalinurellus wieneckii(De Man, 1881) (Decapoda, Achelata, Palinuridae). ACTA ACUST UNITED AC 2013; 25:295-7. [DOI: 10.3109/19401736.2013.796521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol 2013. [DOI: 10.1016/j.ympev.2012.11.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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17
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Marxen JC, Pick C, Kwiatkowski M, Burmester T. Molecular characterization and evolution of haemocyanin from the two freshwater shrimps Caridina multidentata (Stimpson, 1860) and Atyopsis moluccensis (De Haan, 1849). J Comp Physiol B 2013; 183:613-24. [PMID: 23338600 DOI: 10.1007/s00360-013-0740-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 11/22/2012] [Accepted: 12/29/2012] [Indexed: 01/28/2023]
Abstract
Haemocyanin (Hc) is a copper-containing respiratory protein, floating freely dissolved in the hemolymph of many arthropod species. A typical haemocyanin is a hexamer or oligohexamer of six identical or similar subunits, with a molecular mass around 75 kDa each. In the crustaceans, the haemocyanins appear to be restricted to the remipedes and the malacostracans. We have investigated the haemocyanins of two freshwater shrimps, the Amano shrimp Caridina multidentata and the bamboo shrimp Atyopsis moluccensis. We obtained three full-length and one partial cDNA sequences of haemocyanin subunits from the Amano shrimp, which were assigned to the α- and γ-types of decapod haemocyanin subunits. Three complete and two partial haemocyanin cDNA sequences were obtained from the bamboo shrimp, which represent subunit types α, β and γ. This is the first time that sequences of all three subunit types of the decapod haemocyanins were obtained from a single species. However, mass spectrometry analyses identified only α- and γ-type subunits, suggesting that a β-subunit is not a major component of the native haemocyanin of the bamboo shrimp. Phylogenetic and molecular clock analyses showed that malacostracan haemocyanins commenced to diversify into distinct subunit types already ~515 million years ago. β-subunits diverged first, followed by α- and γ-type subunits ~396 million years ago. The haemocyanins of phyllocarids and peracarids form distinct clades within the α/γ-cluster. Within the Caridea, an early divergence of distinct α-type subunits occurred ~200 MYA. The tree of the γ-subunits suggests a common clade of the Caridea (shrimps) and Penaeidae (prawns).
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Affiliation(s)
- Julia C Marxen
- Institute of Zoology and Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
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Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. BMC Genomics 2012; 13:631. [PMID: 23153176 PMCID: PMC3533576 DOI: 10.1186/1471-2164-13-631] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. RESULTS We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. CONCLUSIONS Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.
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Johansson ML, Sremba AL, Feinberg LR, Banks MA, Peterson WT. The mitochondrial genomes of Euphausia pacifica and Thysanoessa raschii sequenced using 454 next-generation sequencing, with a phylogenetic analysis of their position in the Malacostracan family tree. Mol Biol Rep 2012; 39:9009-21. [PMID: 22733485 DOI: 10.1007/s11033-012-1772-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 06/09/2012] [Indexed: 11/29/2022]
Abstract
Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological links, we sequenced the mitochondrial genomes of two species of North Pacific krill, Euphausia pacifica and Thysanoessa raschii, using long-range PCR and 454 GS Junior next-generation sequencing technology. The E. pacifica mitogenome (14,692 + base pairs (bp)) encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and at least 22 transfer RNA (tRNA) genes. The T. raschii mitogenome (14,240 + bp) encodes 13 PCGs, two rRNA genes, and at least 19 tRNA genes. The gene order in both species is similar to that of E. superba. Comparisons between Bering Sea and Yellow Sea E. pacifica revealed a total of 644 variable sites. The most variable protein-coding gene were atp8 (7.55 %, 12 of 159 sites variable), nad4 (6.35 %, 85 variable sites) and nad6 (6.32 %, 33 variable sites). Phylogenetic analyses to assess the phylogenetic position of the Euphausiacea, using the concatenated nucleic acid sequences of E. pacifica and T. raschii along with 46 previously published malacostracan mitogenomes, support the monophyly of the order Decapoda and indicate that the Euphausiacea share a common ancestor with the Decapoda. Future research should utilize this sequence data to explore the population genetics and molecular ecology of these species.
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Affiliation(s)
- Mattias L Johansson
- Cooperative Institute for Marine Resources Studies, Oregon State University, Newport, OR, USA.
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The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:201-11. [DOI: 10.1016/j.cbd.2012.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/21/2012] [Accepted: 02/27/2012] [Indexed: 11/23/2022]
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Kim S, Kim T, Choi HG, Park JK, Ahn DH, Min GS. The complete mitochondrial genome of the Japanese mud shrimp Upogebia major (Crustacea, Decapoda). ACTA ACUST UNITED AC 2012; 22:94-6. [PMID: 22040075 DOI: 10.3109/19401736.2011.624609] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined a full-length sequence of mitochondrial (mt) genome from Upogebia major. This is the first complete mt genome report for infraorder Thalassinidea in Decapoda, Crustacea. Our result showed that U. major generally followed a typical pancrustacean gene order but some tRNA genes showed a very unique gene arrangement such as duplication or translocation. Since none of the complete mt genome sequences in the infraorder Thalassinidea are available yet, this report will provide additional information in relation to mt genome diversity and evolution of the decapods.
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Affiliation(s)
- Sanghee Kim
- Korea Polar Research Institute , Songdo Techno Park, Yeonsu-gu, Incheon 406-840, South Korea.
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Kim S, Park MH, Jung JH, Ahn DH, Sultana T, Kim S, Park JK, Choi HG, Min GS. The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00534.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Assessing population-level variation in the mitochondrial genome of Euphausia superba using 454 next-generation sequencing. Mol Biol Rep 2012; 39:5755-60. [DOI: 10.1007/s11033-011-1385-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/16/2011] [Indexed: 11/26/2022]
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Reimann A, Richter S, Scholtz G. Phylogeny of the Anomala (Crustacea, Decapoda, Reptantia) based on the ossicles of the foregut. ZOOL ANZ 2011. [DOI: 10.1016/j.jcz.2011.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kim S, Lee SH, Park MH, Choi HG, Park JK, Min GS. The complete mitochondrial genome of the American lobster,Homarus americanus(Crustacea, Decapoda). ACTA ACUST UNITED AC 2011; 22:47-9. [DOI: 10.3109/19401736.2011.597389] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Cheng R, Zheng X, Lin X, Yang J, Li Q. Determination of the complete mitochondrial DNA sequence of Octopus minor. Mol Biol Rep 2011; 39:3461-70. [PMID: 21710247 DOI: 10.1007/s11033-011-1118-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 06/20/2011] [Indexed: 01/31/2023]
Abstract
In this study, we have determined the complete nucleotide sequence of the mitochondrial genome of Octopus minor. It is 15,974 nucleotide pairs and encodes 13 proteins, two ribosomal RNAs and 22 tRNAs of the mitochondrion's own protein synthesizing system. Seven of thirteen proteins are encoded by the H-strand, while the other six proteins, as well as the two ribosomal RNAs are encoded by the L-strand. The nucleotide composition of the proteins showed a nucleotide bias against G encoded by the H-strand, while they showed a nucleotide bias against A and C encoded by the L-strand. Two of the 13 protein coding genes of O. minor began with the unorthodox translation initiation codon ATA and all others use the standard ATG. In addition, six of thirteen mt proteins of O. minor have unambiguous termination codons. There are four cases where tRNA genes appear to overlap. The long noncoding region (LNCR) of O. minor was 930 nucleotides and no repeated sequences were found in this LNCR. The gene arrangements of O. minor showed remarkable similarity to that of O. ocellatus and O. vulgaris. Phylogenetic analysis demonstrated that O. minor appears as sister taxan to the monophyletic group combined by O. ocellatus and O. vulgaris, suggesting a relative distant genetic relationship between O. minor and the other two octopus species.
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Affiliation(s)
- Rubin Cheng
- Fisheries College, Ocean University of China, Qingdao, 266003, China
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Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics. Mol Biol Rep 2010; 38:1103-14. [DOI: 10.1007/s11033-010-0207-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
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