1
|
Wang C, Ye P, Pillans R, Chen X, Wang J, Feutry P. Evolution of the Critically Endangered Green Sawfish Pristis zijsron (Rhinopristiformes, Pristidae), Inferred from the Whole Mitochondrial Genome. Genes (Basel) 2023; 14:2052. [PMID: 38002995 PMCID: PMC10671267 DOI: 10.3390/genes14112052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome is 16,804 bp, with a nucleotide composition of 32.0% A, 24.8% C, 13.1% G, and 30.0% T. It contains 37 genes in the typical gene order of fish. Two start (GTG and ATG) and two stop (TAG and TAA/T-) codons are found in the thirteen protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicates that the family Pristidae are suffering a purifying selection. The reconstruction of Bayesian inference and the maximum likelihood phylogenetic tree show the same topological structure, and the family Pristidae is a monophyletic group with strong posterior probability. Pristis zijsron and P. pectinata form a sister group in the terminal clade. And the divergence time of Rhinopristiformes show that P. zijsron and P. pectinata diverged as two separate species in about Paleogene 31.53 Mya. Complete mitochondrial genomes of all five sawfishes have been published and phylogenetic relationships have been analyzed. The results of our study will provide base molecular information for subsequent research (e.g., distribution, conservation, phylogenetics, etc.) on this endangered group.
Collapse
Affiliation(s)
- Chen Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Peiyuan Ye
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Richard Pillans
- CSIRO Environment, Boggo Road, Dutton Park, QLD 4102, Australia;
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Pierre Feutry
- CSIRO Environment, Castray Esplanade, Hobart, TAS 7000, Australia
| |
Collapse
|
2
|
Kundu S, Palimirmo FS, Kang HE, Kim AR, Lee SR, Gietbong FZ, Song SH, Kim HW. Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean. BIOLOGY 2023; 12:1317. [PMID: 37887027 PMCID: PMC10604034 DOI: 10.3390/biology12101317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
Collapse
Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Flandrianto Sih Palimirmo
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Se Hyun Song
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyun-Woo Kim
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| |
Collapse
|
3
|
Fan D, Zhang C, Wang H, Wei Q, Cai H, Wei F, Bian Z, Liu W, Wang X, Liu Z. Fabrication of a composite 3D-printed titanium alloy combined with controlled in situ drug release to prevent osteosarcoma recurrence. Mater Today Bio 2023; 20:100683. [PMID: 37346395 PMCID: PMC10279918 DOI: 10.1016/j.mtbio.2023.100683] [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: 02/12/2023] [Revised: 04/28/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023] Open
Abstract
Osteosarcoma is a malignant bone tumor occurring in adolescents. Surgery combined with adjuvant or neoadjuvant chemotherapy is the standard treatment. However, systemic chemotherapy is associated with serious side effects and a high risk of postoperative tumor recurrence, leading to a high amputation rate and mortality in cancer patients. Implant materials that can simultaneously repair large bone defects and prevent osteosarcoma recurrence are in urgent need. Herein, an intelligent system comprising 3D-printed titanium scaffold (TS) and pH-responsive PEGylated paclitaxel prodrugs was fabricated for bone defect reconstruction and recurrence prevention following osteosarcoma surgery. The drug-loaded implants exhibited excellent stability and biocompatibility for supporting the activity of bone stem cells under normal body fluid conditions and the rapid release of drugs in response to faintly acidic environments. An in vitro study demonstrated that five human osteosarcoma cell lines could be efficiently eradicated by paclitaxel released in an acidic microenvironment. Using mice models, we demonstrated that the drug-loaded TS can enable a pH-responsive treatment of postoperative tumors and effectively prevent osteosarcoma recurrence. Therefore, local implantation of this composite scaffold may be a promising topical therapeutic method to prevent osteosarcoma recurrence.
Collapse
Affiliation(s)
- Daoyang Fan
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, China
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Peking University, Beijing, 100035, China
| | - Chaoqi Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hufei Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingguang Wei
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, China
| | - Hong Cai
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, China
| | - Feng Wei
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, China
| | - Zhilei Bian
- Department of Hematology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Weifeng Liu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Peking University, Beijing, 100035, China
| | - Xing Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongjun Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, China
| |
Collapse
|
4
|
Wang C, Lai T, Ye P, Yan Y, Feutry P, He B, Huang Z, Zhu T, Wang J, Chen X. Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae. Gene 2022; 820:146232. [PMID: 35114282 DOI: 10.1016/j.gene.2022.146232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023]
Abstract
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
Collapse
Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
| | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Peiyuan Ye
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yunrong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning 530000, China
| | | | - Ting Zhu
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; Guangxi Mangrove Research Center, Beihai 536000, China.
| |
Collapse
|
5
|
Wang C, Ye P, Liu M, Zhang Y, Feng H, Liu J, Zhou H, Wang J, Chen X. Comparative Analysis of Four Complete Mitochondrial Genomes of Epinephelidae (Perciformes). Genes (Basel) 2022; 13:genes13040660. [PMID: 35456466 PMCID: PMC9029768 DOI: 10.3390/genes13040660] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 01/19/2023] Open
Abstract
Groupers are commercial, mainly reef-associated fishes, classified in the family Epinephelidae (Perciformes). This study first sequenced the complete mitogenomes of Cephalopholis leopardus, Cephalopholis spiloparaea, Epinephelus amblycephalus, and Epinephelus hexagonatus. The lengths of the four Epinephelidae mitogenomes ranged from 16,585 base pair (bp) to 16,872 bp with the typical gene order. All tRNA genes had a typical cloverleaf structure, except the tRNA-Ser (AGY) gene which was lacking the entire dihydrouridine arm. The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicated that four groupers were suffering a purifying selection. Phylogenetic relationships were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all mitogenomic data of 41 groupers and 2 outgroups. The identical topologies result with high support values showed that Cephalopholis and Epinephelus are not monophyletic genera. Anyperodon and Cromileptes clustered to Epinephelus. Aethaloperca rogaa and Cephalopholis argus assembled a clad. Cephalopholis leopardus, C. spiloparaea, and Cephalopholis miniata are also in a clade. Epinephelushexagonatus is close to Epinephelus tauvina and Epinephelus merra, and E. amblycephalus is a sister group with Epinephelus stictus. More mitogenomic data from Epinephelidae species are essential to understand its taxonomic status with the family Serranidae.
Collapse
Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (P.Y.); (Y.Z.); (H.F.); (J.L.)
| | - Peiyuan Ye
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (P.Y.); (Y.Z.); (H.F.); (J.L.)
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Min Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361012, China;
| | - Yue Zhang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (P.Y.); (Y.Z.); (H.F.); (J.L.)
| | - Haiqing Feng
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (P.Y.); (Y.Z.); (H.F.); (J.L.)
| | - Jingyu Liu
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (P.Y.); (Y.Z.); (H.F.); (J.L.)
| | - Haolang Zhou
- Guangxi Mangrove Research Center, Beihai 536000, China;
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Correspondence: (J.W.); (X.C.); Tel.: +86-137-9817-8534 (J.W.); +86-139-2210-4624 (X.C.)
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (P.Y.); (Y.Z.); (H.F.); (J.L.)
- Guangxi Mangrove Research Center, Beihai 536000, China;
- Correspondence: (J.W.); (X.C.); Tel.: +86-137-9817-8534 (J.W.); +86-139-2210-4624 (X.C.)
| |
Collapse
|
6
|
Zuo Q, Zhang Z, Shen Y. Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda. Ecol Evol 2022; 12:e8764. [PMID: 35356579 PMCID: PMC8948135 DOI: 10.1002/ece3.8764] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/29/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: "TD (N\R) L + C" based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.
Collapse
Affiliation(s)
- Qing Zuo
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Zhisheng Zhang
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Yanjun Shen
- Chongqing Key Laboratory of Animal BiologySchool of Life SciencesChongqing Normal UniversityChongqingChina
| |
Collapse
|
7
|
Huang X, Zhou Z, Lai T, He B, Zhang D. Characterization of the complete mitochondrial genome of blacktip shark Carcharhinus limbatus (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA B Resour 2022; 7:385-386. [PMID: 35187238 PMCID: PMC8856099 DOI: 10.1080/23802359.2021.1914214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this study, we aimed to determine the complete mitochondrial genome of blacktip shark Carcharhinus limbatus. The mitochondrial genome was 16,705 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis was done using the Bayesian inference method, which showed a close relationship between C. limbatus and C. amblyrhynchoides.
Collapse
Affiliation(s)
- Xiaolin Huang
- School of Marine Sciences, Ningbo University, Ningbo, China
- Zhejiang Mariculture Research Institute, Wenzhou, China
| | | | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning, China
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
| |
Collapse
|