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Xu W, Tai J, He K, Xu T, Zhang G, Xu B, Liu H. Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis. Animals (Basel) 2024; 14:1598. [PMID: 38891645 PMCID: PMC11171051 DOI: 10.3390/ani14111598] [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: 04/28/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial genomes (mitogenomes) from four Nannostomus species for the first time. The four mitogenomes exhibited the typical circular structure, with overall sizes varying from 16,661 bp to 16,690 bp. They contained 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 1 control region (CR). Nucleotide composition analysis suggested that the mitochondrial sequences were biased toward A and T. Bayesian inference and maximum likelihood analyses based on PCGs support the family Lebiasinidae classification, described using four Nannostomus species, clustering together with Lebiasina multimaculata from the same family. The results of this study support the current taxonomic classification of the family Lebiasinidae. Phylogenetic analysis also suggested that gene rearrangement would not significantly impact the phylogenetic relationships within the order Characiformes. These results might provide new data regarding the phylogeny and classification of the order Characiformes, thus providing a theoretical basis for the economic development of aquarium fish markets.
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Affiliation(s)
- Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Jingzhe Tai
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Ke He
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China;
| | - Tangjun Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Gaoji Zhang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Boyu Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
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Kavalco KF, Pasa R. Chromosomal Radiation: A model to explain karyotypic diversity in cryptic species. Genet Mol Biol 2023; 46:e20230116. [PMID: 37815421 PMCID: PMC10563172 DOI: 10.1590/1678-4685-gmb-2023-0116] [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: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
We present a concept that explains the pattern of occurrence of widely distributed organisms with large chromosomal diversity, large or small molecular divergence, and the insufficiency or absence of morphological identity. Our model is based on cytogenetic studies associated with molecular and biological data and can be applied to any lineage of sister species, chronospecies, or cryptic species. Through the evaluation of the karyotypic macrostructure, as the physical location of genes e satellites DNAs, in addition to phylogenetic reconstructions from mitochondrial and nuclear genes, per example, we have observed morphologically indistinguishable individuals presenting different locally fixed karyomorphs with phylogeographic discontinuity. The biological process behind this pattern is seen in many groups of cryptic species, in which variation lies mainly in the organization of their genomes but not necessarily in the ecosystems they inhabit or in their external morphology. It's similar to the processes behind other events observed in the distribution of lineages. In this work, we explore the hypothesis of a process analogous to ecological-evolutionary radiation, which we called Chromosomal Radiation. Chromosomal Radiation can be adaptive or non-adaptive and applied to different groups of organisms.
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Affiliation(s)
- Karine Frehner Kavalco
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Genética Ecológica e Evolutiva (LaGEEvo), Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Bioinformática e Genômica, Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
| | - Rubens Pasa
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Genética Ecológica e Evolutiva (LaGEEvo), Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Bioinformática e Genômica, Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
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Liu Q, Yuan H, Xu J, Cui D, Xiong G, Schwarzacher T, Heslop-Harrison JS. The mitochondrial genome of the diploid oat Avena longiglumis. BMC PLANT BIOLOGY 2023; 23:218. [PMID: 37098475 PMCID: PMC10131481 DOI: 10.1186/s12870-023-04217-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species. RESULTS The complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100-31,235 bp) and medium (144-792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts. CONCLUSIONS Comparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Hongyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaxin Xu
- College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gui Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK.
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Rodrigues-Oliveira IH, Pasa R, Menegidio FB, Kavalco KF. Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family. Genomics Inform 2023; 21:e10. [PMID: 37037468 PMCID: PMC10085734 DOI: 10.5808/gi.22041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/14/2023] [Indexed: 04/03/2023] Open
Abstract
The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.
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Affiliation(s)
- Igor Henrique Rodrigues-Oliveira
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Corresponding author: E-mail:
| | - Rubens Pasa
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
| | - Fabiano Bezerra Menegidio
- Technological Research Center, University of Mogi das Cruzes, Mogi das Cruzes 08780-911, Brazil
- Integrated Biotechnology Center, University of Mogi das Cruzes, Mogi das Cruzes 08780-911, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
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Alter SE, Arroyave J. Environmental DNA metabarcoding is a promising method for assaying fish diversity in cenotes of the Yucatán Peninsula, Mexico. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.89857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The karst aquifer of the Yucatán Peninsula (YP) in southeastern Mexico is a unique ecosystem in which water-filled sinkholes, locally known as cenotes, connect subterranean waters with the surface. This system is home to around 20 species of freshwater fishes, including several that are endemic and/or threatened. Studies on this unique ichthyofauna have been partially hampered by the technical difficulties associated with sampling these habitats, particularly submerged caves. In this proof-of-concept study, we use environmental DNA (eDNA) metabarcoding to survey the diversity of freshwater fishes associated with the YP karst aquifer by sampling six cenotes from across the Ring of Cenotes region in northwestern Yucatán, a 180-km-diameter semicircular band of abundant karst sinkholes. Through a combination of conventional sampling (direct observation, fishing) and eDNA metabarcoding, we detected eight species of freshwater fishes across the six sampled cenotes. Overall, our eDNA metabarcoding approach was effective at detecting the presence of fishes from cenote water samples, including one of the two endemic cave-dwelling fish species restricted to the subterranean section of the aquifer. Although our study was focused on detecting fishes via eDNA, we also recovered DNA from several other vertebrate groups, particularly bats. These results suggest that the eDNA metabarcoding approach represents a promising and largely noninvasive method to assay aquatic biodiversity in these vulnerable habitats, allowing more effective, frequent, and wide-ranging surveys. Our detection of DNA from aerial and terrestrial vertebrate fauna implies that eDNA from cenotes, besides being a means to survey aquatic fauna, may also offer an effective way to quickly survey non-aquatic biodiversity associated with these persistent water bodies.
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Comparative mitochondrial genomics of tetras: insights into phylogenetic relationships in Characidae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01195-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Goes CAG, dos Santos RZ, Aguiar WRC, Alves DCV, Silva DMZDA, Foresti F, Oliveira C, Utsunomia R, Porto-Foresti F. Revealing the Satellite DNA History in Psalidodon and Astyanax Characid Fish by Comparative Satellitomics. Front Genet 2022; 13:884072. [PMID: 35801083 PMCID: PMC9253505 DOI: 10.3389/fgene.2022.884072] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic genomes are usually enriched in repetitive DNA sequences, which can be classified as dispersed or tandemly repeated elements. Satellite DNAs are noncoding monomeric sequences organized in a head-to-tail fashion that are generally located on the subtelomeric and/or pericentromeric heterochromatin. In general, a single species incorporates a diverse group of satellite DNA families, which collection is called satellitome. Here, we characterized three new satellitomes from distinct characid fish (Psalidodon fasciatus, P. bockmanni, and Astyanax lacustris) using a combination of genomic, cytogenetic, and bioinformatic protocols. We also compared our data with the available satellitome of P. paranae. We described 57 satellite DNA (satDNA) families of P. fasciatus (80 variants), 50 of P. bockmanni (77 variants), and 33 of A. lacustris (54 variants). Our analyses demonstrated that several sequences were shared among the analyzed species, while some were restricted to two or three species. In total, we isolated 104 distinctive satDNA families present in the four species, of which 10 were shared among all four. Chromosome mapping revealed that the clustered satDNA was mainly located in the subtelomeric and pericentromeric areas. Although all Psalidodon species demonstrated the same pattern of clusterization of satDNA, the number of clusters per genome was variable, indicating a high dynamism of these sequences. In addition, our results expand the knowledge of the As51 satellite DNA family, revealing that P. bockmanni and P. paranae exhibited an abundant variant of 39 bp, while P. fasciatus showed a variant of 43 bp. The majority of satDNAs in the satellitomes analyzed here presented a common library repetitive sequence in Psalidodon and Astyanax, with abundance variations in each species, as expected for closely related groups. In addition, we concluded that the most abundant satDNA in Psalidodon (As51) passed through a diversification process in this group, resulting in new variants exclusive of Psalidodon.
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Affiliation(s)
- Caio Augusto Gomes Goes
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
| | - Rodrigo Zeni dos Santos
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
| | - Weidy Rozendo Clemente Aguiar
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
| | - Dálete Cássia Vieira Alves
- Instituto de Ciências Biológicas e da Saude, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | | | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Instituto de Biociências, Botucatu, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Instituto de Biociências, Botucatu, Brazil
| | - Ricardo Utsunomia
- Instituto de Ciências Biológicas e da Saude, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Fabio Porto-Foresti
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
- *Correspondence: Fabio Porto-Foresti,
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