FishMitoCleaner: Automated Stop Codon Processing and Quality Control of Fish Mitochondrial Protein-Coding Sequences.

IF 2.6 2区生物学 Q2 ECOLOGY

Ecology and Evolution Pub Date : 2026-10-18 eCollection Date: 2026-10-01 DOI:10.1002/ece3.74557

Shaoyu Yang, Peng Xu, Jingzhen Wang, Xiaohui Cai

{"title":"FishMitoCleaner: Automated Stop Codon Processing and Quality Control of Fish Mitochondrial Protein-Coding Sequences.","authors":"Shaoyu Yang, Peng Xu, Jingzhen Wang, Xiaohui Cai","doi":"10.1002/ece3.74557","DOIUrl":null,"url":null,"abstract":"Vertebrate mitochondrial protein-coding genes follow a different genetic code, in which TGA encodes tryptophan and a large number of genes terminate with incomplete stop codons completed post-transcriptionally via polyadenylation. These features are often mishandled when coding sequences (CDS) downloaded from public databases are processed with standard tools, resulting in errors in downstream codon usage and evolution. Here we present FishMitoCleaner, a Python command line tool automating quality control and normalisation of fish mitochondrial CDS sequences in five steps: character validation, internal stop codon scanning, terminal TGA detection, stop codon processing and length normalisation. FishMitoCleaner cleaned 97.6% of input sequences in 22 fish species representing 7 orders and all 13 mitochondrial protein coding genes. Statistical comparison of RSCU values confirmed no bias in codon usage analysis (Welch's t-test, all p > 0.05). FishMitoCleaner is a Python command that allows researchers in aquatic biology and fisheries science to perform rigorous and reproducible CDS quality control in a single command, and clean sequences ready to be analysed in downstream analyses. FishMitoCleaner is also applicable to mitochondrial CDS data from other vertebrate taxa.","PeriodicalId":11467,"journal":{"name":"Ecology and Evolution","volume":"16 10","pages":"e74557"},"PeriodicalIF":2.6000,"publicationDate":"2026-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13677282/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Ecology and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/ece3.74557","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2026/10/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"ECOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Vertebrate mitochondrial protein-coding genes follow a different genetic code, in which TGA encodes tryptophan and a large number of genes terminate with incomplete stop codons completed post-transcriptionally via polyadenylation. These features are often mishandled when coding sequences (CDS) downloaded from public databases are processed with standard tools, resulting in errors in downstream codon usage and evolution. Here we present FishMitoCleaner, a Python command line tool automating quality control and normalisation of fish mitochondrial CDS sequences in five steps: character validation, internal stop codon scanning, terminal TGA detection, stop codon processing and length normalisation. FishMitoCleaner cleaned 97.6% of input sequences in 22 fish species representing 7 orders and all 13 mitochondrial protein coding genes. Statistical comparison of RSCU values confirmed no bias in codon usage analysis (Welch's t-test, all p > 0.05). FishMitoCleaner is a Python command that allows researchers in aquatic biology and fisheries science to perform rigorous and reproducible CDS quality control in a single command, and clean sequences ready to be analysed in downstream analyses. FishMitoCleaner is also applicable to mitochondrial CDS data from other vertebrate taxa.

查看原文本刊更多论文

fishmitoccleaner：鱼类线粒体蛋白编码序列的自动停止密码子处理和质量控制。

脊椎动物线粒体蛋白编码基因遵循不同的遗传密码，其中TGA编码色氨酸，大量基因以转录后通过聚腺苷酸化完成的不完整终止密码子终止。当使用标准工具处理从公共数据库下载的编码序列（CDS）时，通常会错误地处理这些特征，从而导致下游密码子的使用和进化错误。FishMitoCleaner是一个Python命令行工具，可通过五个步骤自动化鱼线粒体CDS序列的质量控制和规范化：字符验证、内部停止密码子扫描、末端TGA检测、停止密码子处理和长度规范化。fishmitoccleaner清洗了22种鱼类的97.6%的输入序列，代表了7个目和全部13个线粒体蛋白编码基因。RSCU值的统计比较证实密码子使用分析无偏倚（Welch’st检验，p < 0.05）。fishmitoccleaner是一个Python命令，允许水生生物学和渔业科学的研究人员在一个命令中执行严格和可重复的CDS质量控制，并清洁序列，准备在下游分析中进行分析。fishmitoccleaner也适用于其他脊椎动物类群的线粒体CDS数据。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Ecology and Evolution ECOLOGY-

CiteScore

4.40

自引率

3.80%

发文量

1027

审稿时长

3-6 weeks

期刊介绍： Ecology and Evolution is the peer reviewed journal for rapid dissemination of research in all areas of ecology, evolution and conservation science. The journal gives priority to quality research reports, theoretical or empirical, that develop our understanding of organisms and their diversity, interactions between them, and the natural environment. Ecology and Evolution gives prompt and equal consideration to papers reporting theoretical, experimental, applied and descriptive work in terrestrial and aquatic environments. The journal will consider submissions across taxa in areas including but not limited to micro and macro ecological and evolutionary processes, characteristics of and interactions between individuals, populations, communities and the environment, physiological responses to environmental change, population genetics and phylogenetics, relatedness and kin selection, life histories, systematics and taxonomy, conservation genetics, extinction, speciation, adaption, behaviour, biodiversity, species abundance, macroecology, population and ecosystem dynamics, and conservation policy.