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González-Delgado S, Rodríguez-Flores PC, Giribet G. Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia). Mol Phylogenet Evol 2024; 198:108129. [PMID: 38878989 DOI: 10.1016/j.ympev.2024.108129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/15/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.
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Affiliation(s)
- Sara González-Delgado
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Santa Cruz de Tenerife, Canary Islands, Spain; Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paula C Rodríguez-Flores
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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2
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Xu H, Zhu Z, Tian Z, Wei C, Fan Q, Wang Y, Shen S, Deng G, Ding M. The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae. Genes (Basel) 2024; 15:111. [PMID: 38255000 PMCID: PMC10815617 DOI: 10.3390/genes15010111] [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: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.
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Affiliation(s)
- Hui Xu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ziyi Zhu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zeyuan Tian
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Cuiyuan Wei
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qi Fan
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanbing Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Shikang Shen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Gang Deng
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
| | - Mingliang Ding
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Food Crops Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650200, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100083, China
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3
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Jiang X, Miao J, Li J, Ye Y. Characterization of Lophiotoma leucotropis Mitochondrial Genome of Family Turridae and Phylogenetic Considerations within the Neogastropoda. Animals (Basel) 2024; 14:192. [PMID: 38254362 DOI: 10.3390/ani14020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Neogastropoda is a group of marine organisms with an extremely wide distribution that is rich in species and economic and ornamental values, the classification of species in this order has been ongoing for a long time, but there is still a great controversy about whether this order is monophyletic. In this study, we obtained the complete mitogenome of Lophiotoma leucotropis by next-generation sequencing and analyzed the basic structural features of the genome, and we found that the number of genes was consistent with that of most of the Neogastropoda snails, containing 37 genes, including 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs. Analyzing base content, amino acid content, codon usage preference, and tRNA structure, the mitogenomes of eight species of Turridae were selected for analysis of selection pressures, and it was found that the evolution of species in this family was affected by purifying selection. In addition, by analyzing the rearrangement characteristics, it was found that the sequence of L. leucotropis was consistent with the Conoidea consensus order, and four of the eight species involved in the analysis showed rearrangements. Finally, we constructed a phylogenetic tree by combining PCGs of 60 species within Caenogastropoda and found Neogastropoda to be a monophyletic group, validating the results of morphological classification. The results will provide more references for the classification and species evolution of Neogastropoda, as well as phylogenetic analysis.
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Affiliation(s)
- Xinqin Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jing Miao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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Xie X, Teng W, Yu Z, Li D, Yang M, Zhang H, Zheng J, Li H, Sun Y, Liu X, Zhou Z, Zhang X, Du S, Li Q, Chang Y, Zhang M, Wang Q. Chromosome-level genome assembly of sea scallop Placopecten magellanicus provides insights into the genetic characteristics and adaptive evolution of large scallops. Genomics 2023; 115:110747. [PMID: 37977331 DOI: 10.1016/j.ygeno.2023.110747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Placopecten magellanicus (Gmelin, 1791), a deep-sea Atlantic scallop, holds significant commercial value as a benthic marine bivalve along the northwest Atlantic coast. Recognizing its economic importance, the need to reconstruct its genome assembly becomes apparent, fostering insights into natural resources and generic breeding potential. This study reports a high-quality chromosome-level genome of P. magellanicus, achieved through the integration of Illumina short read sequencing, PacBio HiFi sequencing, and Hi-C sequencing techniques. The resulting assembly spans 1778 Mb with a scaffold N50 of 86.71 Mb. An intriguing observation arises - the genome size of P. magellanicus surpasses that of its Pectinidae family peers by 1.80 to 2.46 times. Within this genome, 28,111 protein-coding genes were identified. Comparative genomic analysis involving five scallop species unveils the critical determinant of this expanded genome: the proliferation of repetitive sequences recently inserted, contributing to its enlarged size. The landscape of whole genome collinearity sheds light on the relationships among scallop species, enhancing our broader understanding of their genomic framework. This genome provides genomic resources for future molecular biology research on scallops and serves as a guide for the exploration of longevity-related genes in scallops.
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Affiliation(s)
- Xi Xie
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China; Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Dalian, China
| | - Weiming Teng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Zuoan Yu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Dacheng Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Miao Yang
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Haijiao Zhang
- Dalian Changhai-Yide Aquatic Products Co., LTD, Dalian, China
| | - Jie Zheng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Hualin Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Yongxin Sun
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Xiangfeng Liu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Zunchun Zhou
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China; Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Dalian, China
| | - Xiliang Zhang
- Dalian Changhai-Yide Aquatic Products Co., LTD, Dalian, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China.
| | - Ming Zhang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China.
| | - Qingzhi Wang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China; Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Dalian, China.
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5
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Xu M, Li J, Guo B, Xu K, Ye Y, Yan X. Insights into the Deep Phylogeny and Novel Gene Rearrangement of Mytiloidea from Complete Mitochondrial Genome. Biochem Genet 2023; 61:1704-1726. [PMID: 36745306 DOI: 10.1007/s10528-023-10338-4] [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: 07/18/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023]
Abstract
The extant marine mussels which belong to the Mytiloidea are widespread species inhabiting mostly coastal waters, with some distributed in the deep sea. To clarify the classification systems and phylogenetic relationships range from genus to family level within Mytiloidea, new sequence was used in a phylogenetic analysis including all the available Mytiloidea mitochondrial genomes. In this study, the complete mitochondrial genome of Vignadula atrata is 15,624 bp in length and contains 12 protein-coding genes (PCGs, atp8 is absent), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on 12 PCGs showed that it has a close relationship to Bathymodiolus. The analysis of gene rearrangements in the Pteriomorphia showed that the arrangements are highly variable across species, novel gene rearrangements were found within Mytiloidea. The V. atrata mitogenome was provided in detail, with notes on the sequence and a key to the species of Vignadula. This study provides a perspective on the taxonomic histories of the marine mussels and refines the unclear relationship between the origin and evolution of species in Mytiloidea within Bivalvia.
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Affiliation(s)
- Minhui Xu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhejiang Ocean University, Zhoushan, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
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Li F, Zhang Y, Zhong T, Heng X, Ao T, Gu Z, Wang A, Liu C, Yang Y. The Complete Mitochondrial Genomes of Two Rock Scallops (Bivalvia: Spondylidae) Indicate Extensive Gene Rearrangements and Adaptive Evolution Compared with Pectinidae. Int J Mol Sci 2023; 24:13844. [PMID: 37762147 PMCID: PMC10531248 DOI: 10.3390/ijms241813844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the present study, the complete mitochondrial genomes of Spondylus versicolor and S. spinosus were sequenced and compared with those of pectinids. The mtDNA of S. versicolor and S. spinosus show similar patterns with respect to genome size, AT content, AT skew, GC skew, and codon usage, and their mitogenomic sizes are longer than most pectinid species. The mtDNA of S. spinosus is 27,566 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, while an additional tRNA-Met was found in the mtDNA of S. versicolor, which is 28,600 bp in length. The monophylies of Spondylidae and Pectinidae were well supported, but the internal relationships within Pectinidae remain unresolved due to the paraphyly of the genus Mimachlamy and the controversial position of the tribe Aequipectinini. The gene orders of S. versicolor and S. spinosus are almost identical but differ greatly from species of the Pectinidae, indicating extensive gene rearrangements compared with Pectinidae. Positive selection analysis revealed evidence of adaptive evolution in the branch of Spondylidae. The present study could provide important information with which to understand the evolutionary progress of the diverse and economically significant marine bivalve Pectinoidea.
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Affiliation(s)
- Fengping Li
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Yu Zhang
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Tao Zhong
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
| | - Xin Heng
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Tiancheng Ao
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
| | - Zhifeng Gu
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Aimin Wang
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Chunsheng Liu
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Yi Yang
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
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Xu M, Gu Z, Huang J, Guo B, Jiang L, Xu K, Ye Y, Li J. The Complete Mitochondrial Genome of Mytilisepta virgata (Mollusca: Bivalvia), Novel Gene Rearrangements, and the Phylogenetic Relationships of Mytilidae. Genes (Basel) 2023; 14:910. [PMID: 37107667 PMCID: PMC10137486 DOI: 10.3390/genes14040910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The circular mitochondrial genome of Mytilisepta virgata spans 14,713 bp, which contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of the 13 PCGs reveals that the mitochondrial gene arrangement of Mytilisepta is relatively conserved at the genus level. The location of the atp8 gene in Mytilisepta keenae differs from that of other species. However, compared with the putative molluscan ancestral gene order, M. virgata exhibits a high level of rearrangement. We constructed phylogenetic trees based on concatenated 12 PCGs from Mytilidae. As a result, we found that M. virgata is in the same clade as other Mytilisepta spp. The result of estimated divergence times revealed that M. virgata and M. keenae diverged around the early Paleogene period, although the oldest Mytilisepta fossil was from the late or upper Eocene period. Our results provide robust statistical evidence for a sister-group relationship within Mytilida. The findings not only confirm previous results, but also provide valuable insights into the evolutionary history of Mytilidae.
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Affiliation(s)
- Minhui Xu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhongqi Gu
- Shengsi Marine Science and Technology Institute, Shengsi, Zhoushan 202450, China
| | - Ji Huang
- Shengsi Marine Science and Technology Institute, Shengsi, Zhoushan 202450, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lihua Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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8
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Zhang T, Wang Y, Song H. The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei. Genes (Basel) 2023; 14:210. [PMID: 36672951 PMCID: PMC9859601 DOI: 10.3390/genes14010210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.
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Affiliation(s)
- Tianzhe Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101400, China
| | - Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101400, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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9
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Zhang N, Li Y, Halanych KM, Kong L, Li Q. A comparative analysis of mitochondrial ORFs provides new insights on expansion of mitochondrial genome size in Arcidae. BMC Genomics 2022; 23:809. [PMID: 36474182 PMCID: PMC9727918 DOI: 10.1186/s12864-022-09040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arcidae, comprising about 260 species of ark shells, is an ecologically and economically important lineage of bivalve mollusks. Interestingly, mitochondrial genomes of several Arcidae species are 2-3 times larger than those of most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. The large mitochondrial genome size is mainly due to expansion of unassigned regions (regions that are functionally unassigned). Previous work on unassigned regions of Arcidae mtDNA genomes has focused on nucleotide-level analyses to observe sequence characteristics, however the origin of expansion remains unclear. RESULTS We assembled six new mitogenomes and sequenced six transcriptomes of Scapharca broughtonii to identify conserved functional ORFs that are transcribed in unassigned regions. Sixteen lineage-specific ORFs with different copy numbers were identified from seven Arcidae species, and 11 of 16 ORFs were expressed and likely biologically active. Unassigned regions of 32 Arcidae mitogenomes were compared to verify the presence of these novel mitochondrial ORFs and their distribution. Strikingly, multiple structural analyses and functional prediction suggested that these additional mtDNA-encoded proteins have potential functional significance. In addition, our results also revealed that the ORFs have a strong connection to the expansion of Arcidae mitochondrial genomes and their large-scale duplication play an important role in multiple expansion events. We discussed the possible origin of ORFs and hypothesized that these ORFs may originate from duplication of mitochondrial genes. CONCLUSIONS The presence of lineage-specific mitochondrial ORFs with transcriptional activity and potential functional significance supports novel features for Arcidae mitochondrial genomes. Given our observation and analyses, these ORFs may be products of mitochondrial gene duplication. These findings shed light on the origin and function of novel mitochondrial genes in bivalves and provide new insights into evolution of mitochondrial genome size in metazoans.
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Affiliation(s)
- Ning Zhang
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yuanning Li
- grid.27255.370000 0004 1761 1174Shandong University, Qingdao, China
| | - Kenneth M. Halanych
- grid.217197.b0000 0000 9813 0452Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409 USA
| | - Lingfeng Kong
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qi Li
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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10
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Zhang Z, Li J, Zhang X, Lin B, Chen J. Comparative mitogenomes provide new insights into phylogeny and taxonomy of the subfamily Xenocyprinae (Cypriniformes: Cyprinidae). Front Genet 2022; 13:966633. [DOI: 10.3389/fgene.2022.966633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Xenocyprinae is a cyprinid subfamily that not only has a discrete geographic distribution but also has a long history dating to the Early Miocene. However, it is controversial whether systematic classification and some species validity of Xenocyprinae exist, as well as its phylogenetic relationships and evolutionary history. In the present study, we first reviewed the description and taxonomic history of Xenocyprinae, and then the complete mitochondrial genome of Distoechodon compressus, an endemic and locally distributed species belonging to Xenocyprinae, was sequenced and annotated. Finally, all the mitogenomes of Xenocyprinae were compared to reconstruct the phylogenetic relationship and estimate the divergence time. The results showed that the mitogenomes are similar in organization and structure with 16618–16630 bp length from 12 mitogenomes of eight species. Phylogenetic analysis confirmed the monology of Xenocyprinae and illustrated three clades within the Xenocyprinae to consist of ambiguous generic classification. Plagiognathops is a valid genus located at the base of the phylogenetic tree. The genus Xenocypris was originally monophyletic, but X. fangi was excluded. Divergence time estimation revealed that the earliest divergence within Xenocyprinae occurred approximately 12.1 Mya when Plagiognathops separated from the primitive Xenocypris. The main two clades (Xenocypris and (Distoechodon + Pseudobrama + X. fangi)) diverged 10.0 Mya. The major divergence of Xenocyprinae species possibly occurred in the Middle to Late Miocene and Late Pliocene, suggesting that speciation and diversifications could be attributed to the Asian monsoon climate. This study clarifies some controversial issues of systematics and provides essential information on the taxonomy and phylogeny of the subfamily Xenocyprinae.
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11
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Mitochondrial genomes provide insight into interfamilial relationships within Pycnogonida. Polar Biol 2022. [DOI: 10.1007/s00300-022-03085-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family. Mol Biol Rep 2022; 49:9593-9603. [DOI: 10.1007/s11033-022-07857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
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13
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Rapid On-Site Identification for Three Arcidae Species ( Anadara kagoshimensis, Tegillarca granosa, and Anadara broughtonii) Using Ultrafast PCR Combined with Direct DNA Extraction. Foods 2022; 11:foods11162449. [PMID: 36010449 PMCID: PMC9407576 DOI: 10.3390/foods11162449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Granular ark (Tegillarca granosa), broughton's ribbed ark (Anadara broughtonii), and half-crenate ark (Anadara kagoshimensis) are important fishery resources throughout Asia; granular ark exhibiting a higher economic value due to its rarity. However, due to the similar morphological characteristics of the three species, the less valuable species could be exploited for food fraud. In this study, we developed a rapid on-site identification method based on a microfluidic chip for the detection of the three ark shell species. We designed new species-specific primers, targeting the genes encoding mitochondrial cytochrome b or cytochrome c oxidase I, for the identification of the three ark shells and estimated their specificity against 17 species, which amplified only the target species. The sensitivity of each primer was 0.001 ng. In addition, this method was further improved to develop a direct ultrafast polymerase chain reaction (PCR) for on-site food monitoring, which would allow for completing the entire procedure (from sampling to obtaining the results) within 25 min without DNA extraction. Our direct, ultrafast PCR was successfully applied to differentiate the three species from 29 commercial products. Therefore, this assay could be used as a rapid and cost-effective approach for the on-site identification of ark shells in commercial food products.
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14
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Unprecedented frequency of mitochondrial introns in colonial bilaterians. Sci Rep 2022; 12:10889. [PMID: 35764672 PMCID: PMC9240083 DOI: 10.1038/s41598-022-14477-3] [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] [Received: 01/11/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.
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15
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Li Y, Altamia MA, Shipway JR, Brugler MR, Bernardino AF, de Brito TL, Lin Z, da Silva Oliveira FA, Sumida P, Smith CR, Trindade-Silva A, Halanych KM, Distel DL. Contrasting modes of mitochondrial genome evolution in sister taxa of wood-eating marine bivalves (Teredinidae and Xylophagaidae). Genome Biol Evol 2022; 14:evac089. [PMID: 35714221 PMCID: PMC9226539 DOI: 10.1093/gbe/evac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 11/14/2022] Open
Abstract
The bivalve families Teredinidae and Xylophagaidae include voracious consumers of wood in shallow and deep-water marine environments, respectively. The taxa are sister clades whose members consume wood as food with the aid of intracellular cellulolytic endosymbionts housed in their gills. This combination of adaptations is found in no other group of animals and was likely present in the common ancestor of both families. Despite these commonalities, the two families have followed dramatically different evolutionary paths with respect to anatomy, life history and distribution. Here we present 42 new mitochondrial genome sequences from Teredinidae and Xylophagaidae and show that distinct trajectories have also occurred in the evolution and organization of their mitochondrial genomes. Teredinidae display significantly greater rates of amino acid substitution but absolute conservation of protein-coding gene order, whereas Xylophagaidae display significantly less amino acid change but have undergone numerous and diverse changes in genome organization since their divergence from a common ancestor. As with many bivalves, these mitochondrial genomes encode two ribosomal RNAs, 12 protein coding genes, and 22 tRNAs; atp8 was not detected. We further show that their phylogeny, as inferred from amino acid sequences of 12 concatenated mitochondrial protein-coding genes, is largely congruent with those inferred from their nuclear genomes based on 18S and 28S ribosomal RNA sequences. Our results provide a robust phylogenetic framework to explore the tempo and mode of mitochondrial genome evolution and offer directions for future phylogenetic and taxonomic studies of wood-boring bivalves.
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Affiliation(s)
- Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Marvin A Altamia
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
| | - J Reuben Shipway
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Mercer R Brugler
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, South Carolina 29902, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA
| | | | - Thaís Lima de Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Paulo Sumida
- Departamento de Oceanografia Biológica, Instituto Oceanográfico da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Craig R Smith
- Department of Oceanography, University of Hawai’i at Mãnoa, Hawaii, USA
| | - Amaro Trindade-Silva
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, North Carolina, USA
| | - Daniel L Distel
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
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16
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Breton S, Stewart DT, Brémaud J, Havird JC, Smith CH, Hoeh WR. Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system? Bioessays 2022; 44:e2100283. [PMID: 35170770 PMCID: PMC9083018 DOI: 10.1002/bies.202100283] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 01/10/2023]
Abstract
Animal and plant species exhibit an astonishing diversity of sexual systems, including environmental and genetic determinants of sex, with the latter including genetic material in the mitochondrial genome. In several hermaphroditic plants for example, sex is determined by an interaction between mitochondrial cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Specifically, CMS involves aberrant mitochondrial genes that prevent pollen development and specific nuclear genes that restore it, leading to a mixture of female (male-sterile) and hermaphroditic individuals in the population (gynodioecy). Such a mitochondrial-nuclear sex determination system is thought to be rare outside plants. Here, we present one possible case of CMS in animals. We hypothesize that the only exception to the strict maternal mtDNA inheritance in animals, the doubly uniparental inheritance (DUI) system in bivalves, might have originated as a mitochondrial-nuclear sex-determination system. We document and explore similarities that exist between DUI and CMS, and we propose various ways to test our hypothesis.
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Affiliation(s)
- Sophie Breton
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Julie Brémaud
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chase H Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
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17
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Balech B, Sandionigi A, Marzano M, Pesole G, Santamaria M. MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. Database (Oxford) 2022; 2022:6521297. [PMID: 35134858 PMCID: PMC9216479 DOI: 10.1093/database/baab084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 01/05/2023]
Abstract
Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (39.1% unique to BOLD, 3.6% unique to ENA, and 57.2% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats (‘fasta’ for sequences & ‘tsv’ for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines. Database URL: https://github.com/bachob5/MetaCOXI
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Affiliation(s)
- Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
| | - Anna Sandionigi
- Research and Development Department, Quantia Consulting srl, via Francesco Petrarca 20, Mariano Comense 22066, Italy
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, via Orabona 4, Bari 70126, Italy
| | - Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
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18
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The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa. Genes (Basel) 2021; 12:genes12122030. [PMID: 34946978 PMCID: PMC8700879 DOI: 10.3390/genes12122030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.
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19
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Hu Z, Liu S, Xu Z, Liu S, Li T, Yu S, Zhao W. Comparison of
Aspergillus chevalieri
and related species in dark tea at different aspects: Morphology, enzyme activity and mitochondrial genome. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhi‐Yuan Hu
- College of Food Science and Technology Hunan Agricultural University Changsha China
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Su‐Chun Liu
- College of Food Science and Technology Hunan Agricultural University Changsha China
| | - Zheng‐Gang Xu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western College of Forestry Northwest A & F University Yangling China
| | - Shi‐Quan Liu
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Tao‐Tao Li
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Song‐Lin Yu
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Wei‐Ping Zhao
- College of Business Hunan Agricultural University Changsha China
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20
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Teng W, Xie X, Nie H, Sun Y, Liu X, Yu Z, Zheng J, Liu H, Li D, Zhang M, Wang Z, Zhu S, Du S, Du S, Li Q, Wang Q. Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shells. Mol Ecol Resour 2021; 22:295-306. [PMID: 34214251 DOI: 10.1111/1755-0998.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/30/2022]
Abstract
Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we report a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50 = 2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the haemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.
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Affiliation(s)
- Weiming Teng
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Xi Xie
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Yamin Sun
- Tianjin Biochip Corporation, Tianjin, China
| | - Xiangfeng Liu
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Zuoan Yu
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Jie Zheng
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Hongyue Liu
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Dacheng Li
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Ming Zhang
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Zhisong Wang
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Shouwei Zhu
- Jinzhou Research Institute of Science and Technology, Jinzhou, China
| | - Shangkun Du
- Jinzhou Research Institute of Science and Technology, Jinzhou, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qingzhi Wang
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
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21
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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22
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Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
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23
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Wang Y, Yang Y, Liu H, Kong L, Yu H, Liu S, Li Q. Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes. ZOOL SCR 2020. [DOI: 10.1111/zsc.12454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Wang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Yi Yang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hongyue Liu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
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