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Alvarenga M, D'Elia AKP, Rocha G, Arantes CA, Henning F, de Vasconcelos ATR, Solé-Cava AM. Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic. BMC Genomics 2024; 25:215. [PMID: 38413941 PMCID: PMC10898094 DOI: 10.1186/s12864-024-10035-5] [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: 10/27/2023] [Accepted: 01/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae). RESULTS Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit. CONCLUSIONS Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification.
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Affiliation(s)
- Marcela Alvarenga
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Ananda Krishna Pereira D'Elia
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Graciane Rocha
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Clara Alvarez Arantes
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Frederico Henning
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil.
| | | | - Antonio Mateo Solé-Cava
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
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Yi J, Liu J, Mao Y, Cheng Y, Lin M, Xu H, An Y, Li J, Wu H. The Complete Mitochondrial Genome of Chilo infuscatellus (Lepidoptera: Pyralidae), and Related Phylogenetic Analysis. Biochem Genet 2024:10.1007/s10528-023-10639-8. [PMID: 38306003 DOI: 10.1007/s10528-023-10639-8] [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: 08/08/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024]
Abstract
The Chilo infuscatellus (Lepidoptera: Pyralidae) is a significant pest of sugarcane in China. The genome-level characteristics of this pest are important genetic resources for identification, phylogenetic analysis, and even management. In the present study, the complete mitogenome of C. infuscatellus was sequenced and characterized. The assembled mitochondrial genome is 15,252 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Except for the CGA codon for the cox1 gene, the PCGs are initiated with ATN codons (ATG, ATT, and ATA). These PCGs are terminated with TAA or an incomplete termination codon of a single T. Except for the loss of the "DHU" arm for trnS1, the tRNA genes were folded into the typical cloverleaf structure. The A + T-rich region has a high AT content of 96.19% and contains the motifs "ATAGA" and "ATTTA", as well as a 19 bp poly-T stretch and microsatellite regions. The C. infuscatellus mitogenome exhibits a conserved gene order among lepidopteran insects, with a rearrangement of the trnM gene compared to the ancestral insect gene order. Phylogenetic analysis based on the 13 PCGs using Bayesian inference (BI) and maximum likelihood (ML) methods confirmed the monophyly of Pyralidae and Crambidae within Pyraloidea. The relationships between subfamilies in Pyralidae can be described as (Galleriinae + (Phycitinae + (Pyralinae + Epipaschiinae))). The "PS clade" and "non-PS clade" were formed within the family Crambidae. These findings provide valuable genetic resources for the identification, phylogenetic analysis, and management of sugarcane borers, contributing significantly to our understanding of the phylogeny of Pyraloidea insects and their evolution.
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Affiliation(s)
- Jiequn Yi
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jianbai Liu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yongkai Mao
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yinjie Cheng
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Minjiang Lin
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Hanliang Xu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yuxing An
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jihu Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
| | - Han Wu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
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Yang Y, Wang J, Dai R, Wang X. Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae). Genes (Basel) 2023; 14:1175. [PMID: 37372355 DOI: 10.3390/genes14061175] [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: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Krisna species are insects that have piercing-sucking mouthparts and belong to the Krisnini tribe in the Iassinae subfamily of leafhoppers in the Cicadellidae family. In this study, we sequenced and compared the mitochondrial genomes (mitogenomes) of four Krisna species. The results showed that all four mitogenomes were composed of cyclic double-stranded molecules and contained 13 protein-coding genes (PCGs) and 22 and 2 genes coding for tRNAs and rRNAs, respectively. Those mitogenomes exhibited similar base composition, gene size, and codon usage patterns for the protein-coding genes. The analysis of the nonsynonymous substitution rate (Ka)/synonymous substitution rate (Ks) showed that evolution occurred the fastest in ND4 and the slowest in COI. 13 PCGs that underwent purification selection were suitable for studying phylogenetic relationships within Krisna. ND2, ND6, and ATP6 had highly variable nucleotide diversity, whereas COI and ND1 exhibited the lowest diversity. Genes or gene regions with high nucleotide diversity can provide potential marker candidates for population genetics and species delimitation in Krisna. Analyses of parity and neutral plots showed that both natural selection and mutation pressure affected the codon usage bias. In the phylogenetic analysis, all subfamilies were restored to a monophyletic group; the Krisnini tribe is monophyletic, and the Krisna genus is paraphyletic. Our study provides novel insights into the significance of the background nucleotide composition and codon usage patterns in the CDSs of the 13 mitochondrial PCGs of the Krisna genome, which could enable the identification of a different gene organization and may be used for accurate phylogenetic analysis of Krisna species.
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Affiliation(s)
- Yanqiong Yang
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Jiajia Wang
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Renhuai Dai
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Xianyi Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China
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