Progress, challenge and prospect of plant plastome annotation
文献类型：期刊论文
| 作者 | Qu,Xiao-Jian; Zou,Dan; Zhang,Rui-Yu; Stull,Gregory W.; Yi,Ting-Shuang |
| 刊名 | FRONTIERS IN PLANT SCIENCE
 |
| 出版日期 | 2023 |
| 卷号 | 14页码:1166140 |
| 关键词 | annotation standards chloroplast genome plastome protein structure pseudogenes RNA-editing genes MITOCHONDRIAL GENES RNA GENOME SEQUENCE CHLOROPLASTS TRANSLATION |
| DOI | 10.3389/fpls.2023.1166140 |
| 英文摘要 | The plastome (plastid genome) represents an indispensable molecular data source for studying phylogeny and evolution in plants. Although the plastome size is much smaller than that of nuclear genome, and multiple plastome annotation tools have been specifically developed, accurate annotation of plastomes is still a challenging task. Different plastome annotation tools apply different principles and workflows, and annotation errors frequently occur in published plastomes and those issued in GenBank. It is therefore timely to compare available annotation tools and establish standards for plastome annotation. In this review, we review the basic characteristics of plastomes, trends in the publication of new plastomes, the annotation principles and application of major plastome annotation tools, and common errors in plastome annotation. We propose possible methods to judge pseudogenes and RNA-editing genes, jointly consider sequence similarity, customed algorithms, conserved domain or protein structure. We also propose the necessity of establishing a database of reference plastomes with standardized annotations, and put forward a set of quantitative standards for evaluating plastome annotation quality for the scientific community. In addition, we discuss how to generate standardized GenBank annotation flatfiles for submission and downstream analysis. Finally, we prospect future technologies for plastome annotation integrating plastome annotation approaches with diverse evidences and algorithms of nuclear genome annotation tools. This review will help researchers more efficiently use available tools to achieve high-quality plastome annotation, and promote the process of standardized annotation of the plastome. |
| 学科主题 | Plant Sciences |
| WOS记录号 | WOS:001006958300001 |
| 源URL | [http://ir.kib.ac.cn/handle/151853/74981]  |
| 专题 | 中国科学院昆明植物研究所 |
| 推荐引用方式 GB/T 7714 | Qu,Xiao-Jian,Zou,Dan,Zhang,Rui-Yu,et al. Progress, challenge and prospect of plant plastome annotation[J]. FRONTIERS IN PLANT SCIENCE,2023,14:1166140. |
| APA | Qu,Xiao-Jian,Zou,Dan,Zhang,Rui-Yu,Stull,Gregory W.,&Yi,Ting-Shuang.(2023).Progress, challenge and prospect of plant plastome annotation.FRONTIERS IN PLANT SCIENCE,14,1166140. |
| MLA | Qu,Xiao-Jian,et al."Progress, challenge and prospect of plant plastome annotation".FRONTIERS IN PLANT SCIENCE 14(2023):1166140. |
入库方式： OAI收割
来源：昆明植物研究所
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