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Li F, Li W, Zhang Y, Wang A, Liu C, Gu Z, Yang Y. The molecular phylogeny of Caenogastropoda (Mollusca, Gastropoda) based on mitochondrial genomes and nuclear genes. Gene 2024; 928:148790. [PMID: 39053659 DOI: 10.1016/j.gene.2024.148790] [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: 04/07/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Comprising about 60 % of gastropod diversity, caenogastropods display almost all kinds of shell forms and include many commercially important marine groups. Although the monophyly of Caenogastropoda has been widely accepted, thier internal phylogenetic relationships remain unclear. In the present study, a total of 27 caenogastropods belonging to eight superfamilies were sequenced and used for phylogenetic reconstruction. All newly sequenced mitogenomes adhered to the consensus gene order of caenogastropods, except for those of Vanikoroidea, Vermetoidea and Cerithioidea, which involved protein-coding genes. The reconstructed mitogenomic phylogeny suggested the monophylies of Architaenioglossa, Sorbeoconcha, Hypsogastropoda and the siphonate clade. The present study also identified a close affinity among Cypraeoidea, Ficoidea, Tonnoidea, and Neogastropoda, supported by the presence of a pleurembolic proboscis. The monophyly of Neogastropoda was not supported, as Cancellariidae was found to be sister to the limpet-shaped group Calyptraeoidea, and (Tonooidea + Ficoidea) were sister to the remaining neogastropods. This study provides important information for better understanding the evolution of caenogastropods, as well as for the protection and utilization of these diverse and economically significant marine resources.
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Affiliation(s)
- Fengping Li
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Wanying Li
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Yu Zhang
- Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Aimin Wang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Chunsheng Liu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Zhifeng Gu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Yi Yang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China.
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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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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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Qi Y, Zhong Z, Liu X, He X, Zhou Y, Zhang L, Chen C, Linse K, Qiu JW, Sun J. Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda. Mol Phylogenet Evol 2024; 190:107968. [PMID: 38000707 DOI: 10.1016/j.ympev.2023.107968] [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: 09/27/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Patellogastropoda, the true limpets, is a major group of gastropods widely distributed in marine habitats from the intertidal to deep sea. Though important for understanding their evolutionary radiation, the phylogenetic relationships among the patellogastropod families have always been challenging to reconstruct, with contradictory results likely due to insufficient sampling. Here, we obtained mitogenomic and phylogenomic data (transcriptomic or genomic) from six species representing the three predominantly deep-water patellogastropod families: Lepetidae, Neolepetopsidae, and Pectinodontidae. By using various phylogenetic methods, we show that mitogenome phylogeny recovers monophyly of eight families in most of the trees, though the relationships among families remain contentious. Meanwhile, a more robust family-level topology consistent with morphology was achieved by phylogenomics. This also reveals that these mainly deep-water families are monophyletic, suggesting a single colonisation of the deep water around the Jurassic. We also found a lack of significant correlation between genome size and habitat depth, despite some deep-water species exhibiting larger genome sizes. Our phylogenomic tree provides a stable phylogenetic backbone for Patellogastropoda that includes seven of the nine recognized families and paves the way for future evolutionary analyses in this major group of molluscs.
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Affiliation(s)
- Ying Qi
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Zhaoyan Zhong
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Xu Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Xing He
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 311005, China
| | - Lili Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katrin Linse
- British Antarctic Survey, Cambridge, United Kingdom
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Jin Sun
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China.
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Ma P, Liu Y, Wang J, Chen Y, Zhang Z, Zhang T, Wang H. Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications. Int J Biol Macromol 2023; 249:126081. [PMID: 37536404 DOI: 10.1016/j.ijbiomac.2023.126081] [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: 01/27/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.
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Affiliation(s)
- Peizhen Ma
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yumeng Liu
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiahui Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ya Chen
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Haiyan Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, 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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Wei J, Kong L. Taxonomic review of Kaloplocamus from the Yellow Sea, China with the description of a new species (Nudibranchia, Doridina, Polyceridae). Zookeys 2023; 1168:107-129. [PMID: 37415715 PMCID: PMC10320717 DOI: 10.3897/zookeys.1168.101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
Species of Kaloplocamus Bergh, 1880 are enigmatic Nudibranchia sea slugs, and only two valid species are reported in the northwestern Pacific. Kaloplocamusjaponicus (Bergh, 1880) was initially described based on alcohol-fixed specimens. In the latest revision of Kaloplocamus, it was synonymized with Kaloplocamusramosus (Cantraine, 1835). Recently, several nudibranchs were collected from Tianheng, Shandong Province, China, and one of them is identified as an undescribed species described here as Kaloplocamusalbopunctatussp. nov. based on integrated approaches incorporating morphological observations, internal anatomy, and phylogenetic analyses of two mitochondrial (COI, 16S rRNA) genes. The other species is identified as K.japonicus Bergh, 1880 based on the anatomy of the reproductive system. The new species K.albopunctatussp. nov. is similar to K.ramosus in having a bright orange-red color pattern but differs significantly in the structure of appendages and reproductive system. Kaloplocamusjaponicus can be easily distinguished from other Kaloplocamus species by its translucent, white-pink coloration and unique features of the female reproductive organ. Both species are supported as distinct species in all molecular analyses. The phylogenetic analyses propose a new estimate of the relationship between Kaloplocamus and Plocamopherus, and the evolution of bioluminescence within Triophinae is discussed. Our results also suggest cryptic biodiversity within the K.ramosus species complex.
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Affiliation(s)
- Jingcheng Wei
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
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Xu T, Kong L, Li Q. Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case. Genes (Basel) 2022; 13:genes13071192. [PMID: 35885975 PMCID: PMC9318368 DOI: 10.3390/genes13071192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 02/05/2023] Open
Abstract
Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled genome skims, which can effectively improve phylogenetic signal and identification resolution. Studies have shown that the software Skmer and APPLES work well at estimating genomic distance and performing phylogenetic placement in birds and insects using low-coverage genome skims. In this study, we use Skmer and APPLES based on genome skims of 11 patellogastropods to perform assembly-free and alignment-free species identification and phylogenetic placement. Whether or not data corresponding to query species are present in the reference database, Skmer selects the best matching or closest species with COI barcodes under different sizes of genome skims except lacking species belonging to the same family as a query. APPLES cannot place patellogastropods in the correct phylogenetic position when the reference database is sparse. Our study represents the first attempt at assembly-free and alignment-free species identification of marine mollusks using genome skims, demonstrating its feasibility for patellogastropod species identification and flanking the necessity of establishing a database to share genome skims.
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Affiliation(s)
- Tao Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.X.); (Q.L.)
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.X.); (Q.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 5 Yushan Road, Qingdao 266003, China
- Correspondence:
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.X.); (Q.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 5 Yushan Road, Qingdao 266003, China
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De Vivo M, Lee HH, Huang YS, Dreyer N, Fong CL, de Mattos FMG, Jain D, Wen YHV, Mwihaki JK, Wang TY, Machida RJ, Wang J, Chan BKK, Tsai IJ. Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum. Sci Rep 2022; 12:9973. [PMID: 35705661 PMCID: PMC9200733 DOI: 10.1038/s41598-022-14121-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1-18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.
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Affiliation(s)
- Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yu-Sin Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Niklas Dreyer
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Natural History Museum of Denmark, University of Copenhagen, Faculty of Science, Copenhagen, Denmark
| | - Chia-Ling Fong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Felipe Monteiro Gomes de Mattos
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Dharmesh Jain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Yung-Hui Victoria Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
| | - John Karichu Mwihaki
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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