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Deng A, Li J, Yao Z, Afriyie G, Chen Z, Guo Y, Luo J, Wang Z. SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata. Front Genet 2021; 12:741243. [PMID: 34721529 PMCID: PMC8552913 DOI: 10.3389/fgene.2021.741243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/24/2021] [Indexed: 11/24/2022] Open
Abstract
Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata.
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Affiliation(s)
- Aiping Deng
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jinpeng Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zebin Yao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Gyamfua Afriyie
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ziyang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yusong Guo
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jie Luo
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
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Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly. Mol Phylogenet Evol 2019; 135:86-97. [PMID: 30771513 DOI: 10.1016/j.ympev.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 11/22/2022]
Abstract
The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.
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Dong Y, Cao Z, Liang X, Cui J, Wu J, Xie Z, Ji C. [Effectiveness of retro-orbicularis oculi fat resection in Park double eyelid surgery to correct swollen upper eyelid]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2017; 31:996-998. [PMID: 29806440 PMCID: PMC8458585 DOI: 10.7507/1002-1892.201703021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/20/2017] [Indexed: 11/03/2022]
Abstract
Objective To investigate the effectiveness of retro-orbicularis oculi fat resection in Park double eyelid surgery to correct the swollen upper eyelid. Methods Between September 2015 and July 2016, partial resection of the retro-orbicularis oculi fat was performed on 32 cases with bilateral swollen upper eyelids in Park double eyelid surgery. There were 10 males and 22 females with an average age of 25 years (range, 19-32 years). The patients had normal function of the levator muscle, and had no history of double eyelid surgery. Results All the incisions healed by first intention. There was no obvious congestion, swelling, levator muscle dysfunction. All patients were followed up 2-14 months, with an average of 10 months. The double eyelid fold was naturally smooth, without depressed scar; blepharochalasis was obviously improved, and the function of upper eyelid levator muscle was normal. All patients were satisfied with the aesthetic effect. Conclusion Park double eyelid surgery and partial resection of retro-orbicularis oculi fat can effectively improve the aesthetic effect in patients with swollen upper eyelid, and can achieve the perfect function and appearance.
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Affiliation(s)
- Yanhui Dong
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042, P.R.China
| | - Zhe Cao
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042, P.R.China
| | - Xiaoqin Liang
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042,
| | - Jiulin Cui
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042, P.R.China
| | - Jun Wu
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042, P.R.China
| | - Zhiwei Xie
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042, P.R.China
| | - Caixia Ji
- Institute of Reconstructive Plastic Surgery, Weifang Medical University, Weifang Shandong, 261042, P.R.China
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Shen X, Song J, Meng X, Tian M, Yan B, Cheng H, Cai Y, Zhao J. The first representative of Coelomactra antiquata mitochondrial genome from Liaoning (China) and phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:525-527. [PMID: 33473543 PMCID: PMC7800962 DOI: 10.1080/23802359.2016.1197064] [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: 11/18/2022]
Abstract
Coelomactra antiquata is a famous delicacy and a promising new candidate for aquaculture, which belongs to the family Mactridae (Mollusca: Veneroida). The complete mitochondrial genome of C. antiquata (Liao Ning province, in China, LN) was finished, which is the first representative from this province. The results showed that the total length of LN-mtDNA sequence is 16,797 bp and the content of A + T is 65.01%. It encodes 35 genes, including 12 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. All coding genes are encoded on the heavy strand. Compared with the typical gene content of animal mitochondrial genomes, atp8 and trnSer(UCN) genes are missing in the mitochondrial genome. The complete mitochondrial genome contains 26 non-coding regions (1598 bp), one major non-coding region consists of 1046 bp in which 4.9 tandem repeat sequences (99bp per sequence) was observed. The phylogenetic tree showed that Liaoning population was clustered into one clade with Shandong (Rizhao, Jiaonan and Jimo) and Guangxi (Beihai) populations, meanwhile all of them are far from the Fujian populations (Pingtan, Zhangzhou and Changle). So, Liaoning, Shandong and Guangxi populations have a close relationship. Actually, Fujian is located between Liaoning, Shandong and Guangxi. So, the result challenges the previously assumed relevance between geographic distance and genetic distance. The genetic distance of Liaoning C. antiquata and Fujian (Changle, Zhangzhou and Pingtan) C. antiquata (0.176–0.177) is greater than the genetic distance between Mytilus galloprovincialis and Mytilus trossulus (0.160). The genetic difference of Liaoning population and Fujian populations has reached species level.
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Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China.,College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Jun Song
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Xueping Meng
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China
| | - Binlun Yan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China.,College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Hanliang Cheng
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Yuling Cai
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Jun Zhao
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
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Shen X, Meng X, Tian M, Yan B, Cheng H, Lu W, Chai Y. The first mitochondrial genome of Coelomactra antiquata (Mollusca: Veneroida: Mactridae) from Guangxi (China) and potential molecular markers. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3642-3. [PMID: 26329456 DOI: 10.3109/19401736.2015.1079835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Coelomactra antiquata (Guangxi, in China, GX) was determined. It is 16 801 bp in length and is the first representative from this province. The mitochondrial genome encodes 35 genes, including 12 PCGs, two ribosomal RNA, and 21 transfer RNA genes. Atp8 and trnSer(UCN) genes are missing, compared with the typical gene content of animal mitochondrial genomes. Three (cob, nad1, nad4, and nad6) of the 12 PCGs in the mitochondrial genome initiate with the ATA, while other PCGs start with ATG. Two PCGs (atp6 and nad4L) end with incomplete stop codons (T-), and the remaining ones have complete stop codons (TAA or TAG). The largest non-coding region of the C. antiquata (GX) contains one section of tandem repeats (5 × 99 bp). Among all PCGs and rRNAs, the nad5 gene contains the maximum polymorphic sites (430), followed by nad4 (261) and cox2 (240). Two ribosomal RNA genes (srRNA and lrRNA) and cox1 are most conservative. The proportions of polymorphic sites in six genes (nad4, nad2, nad6, nad5, cox2, and nad3) are more than 20% (ranging from 20.25% to 25.21%). These high variable genes can be used as molecular markers in the population genetic analysis of the species.
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Affiliation(s)
- Xin Shen
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China .,b Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology , Lianyungang , China , and.,c Jiangsu Institute of Marine Resources , Lianyungang , China
| | - Xueping Meng
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | - Mei Tian
- b Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology , Lianyungang , China , and
| | - Binlun Yan
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China .,b Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology , Lianyungang , China , and
| | - Hanliang Cheng
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | - Wei Lu
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | - Yuling Chai
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
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Shen X, Meng XP, Chu KH, Zhao NN, Tian M, Liang M, Hao J. Comparative mitogenomic analysis reveals cryptic species: A case study in Mactridae (Mollusca: Bivalvia). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2014; 12:1-9. [PMID: 25247670 DOI: 10.1016/j.cbd.2014.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/17/2022]
Abstract
The Chinese surf clam Mactra chinensis Philippi, 1846 is a commercially important marine bivalve belonging to the family Mactridae (Mollusca: Bivalvia). In this study, the M. chinensis mitochondrial genomic features are analyzed. The genome has 34 genes on the same strand, lacking atp8 and both trnS (trnS1 and trnS2) as compared with the typical gene content of metazoan mitochondrial genomes. The A+T content of M. chinensis mitochondrial genome is 63.72%, which is slightly lower than that of M. veneriformis (67.59%) and Coelomactra antiquata (64.33% and 64.14% for the samples from Ri Zhao, Shandong Province, and Zhang Zhou, Fujian Province, China, respectively) in the same family. There are 22 NCRs in the M. chinensis mitochondrial genome, accounting for 12.91% of the genome length. The longest NCR (1,075bp in length) is located between trnT and trnQ. A TRS (127bp×8.15) accounts for 96.3% (1,035/1,075) of this NCR. The occurrence of TRS in NCR is shared by the two Mactra mitochondrial genomes, but is not found in the two Coelomactra mitochondrial genomes. A phylogenetic tree constructed based on 12 PCGs of 25 bivalve mitochondrial genomes shows that all seven genera (Mactra, Coelomactra, Paphia, Meretrix, Solen, Mytilus, and Crassostrea) constitute monophyletic groups with very high support values. Pairwise genetic distance analyses indicate that the genetic distance of C. antiquata from the two localities is 0.084, which is greater than values between congeneric species, such as those in Mactra, Mytilus, Meretrix, and Crassostrea. The results show that the C. antiquata from the two localities represent cryptic species.
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Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China; Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Xue Ping Meng
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Na Na Zhao
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China; Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Meng Liang
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Jue Hao
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
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