Towards comprehensive integration and curation of chloroplast genomes

Hua, Zhongyi; Tian, Dongmei; Jiang, Chao; Song, Shuhui; Chen, Ziyuan; Zhao, Yuyang; Jin, Yan; Huang, Luqi; Zhang, Zhang; Yuan, Yuan

doi:10.1111/pbi.13923

Cited by 15 publications

(7 citation statements)

References 12 publications

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“…More importantly, we have newly defined a DNA signature sequence (DSS), which is a nucleotide sequence of constant length capable of detecting the presence of an organism (referred to as the target species) and distinguishing it from other species (referred to as the background species). The candidate DSSs are a species-level marker that can be used as a complement to conventional DNA markers (Hua et al 2023 ). All these genetic markers make CGIR a valuable resource for researchers working on phylogenetics and chloroplast genetic engineering.…”

Section: Multi-omics Data Repositoriesmentioning

confidence: 99%

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Tian,

Xu,

Kang

et al. 2024

aBIOTECH

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Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems, including the constituent elements within and among species. Through various efforts in genomic data archiving, integrative analysis and value-added curation, the National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), has successfully established and currently maintains a vast amount of database resources. This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts. Here, we present a comprehensive overview of central repositories dedicated to archiving, presenting, and sharing plant omics data, introduce knowledgebases focused on variants or gene-based functional insights, highlight species-specific multiple omics database resources, and briefly review the online application tools. We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

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Section: Multi-omics Data Repositoriesmentioning

confidence: 99%

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Tian,

Xu,

Kang

et al. 2024

aBIOTECH

Self Cite

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“…We suggest that when annotating the target plastomes, it is necessary to use the plastomes of the species with the highest priority as the reference plastomes, which is similar to the type specimen in species identification. A recently published study generated plastome database with curated plastomes ( Hua et al., 2022 ). It is a good to help researchers to resolve various plastome annotation problems.…”

Section: Challenge and Relevant Solutionsmentioning

confidence: 99%

Progress, challenge and prospect of plant plastome annotation

Zou

Zhang

et al. 2023

Front. Plant Sci.

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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.

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“…Since the sequencing of the first chloroplast genome (plastome) in 1986 [40], there has been rapid progress in high-throughput sequencing technology, resulting in the continuous sequencing of the numerous plant plastomes [41,42]. The National Center for Biotechnology Information (NCBI) organelle genome database currently holds more than 8600 plant plastomes, with the majority of them sequenced in the past four years [43]. In contrast to nuclear genomes, plastomes typically exhibit a conserved structure and a relatively lower rate of nucleotide substitution [44,45].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Chloroplast Genomes for the Genus Manglietia Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution

Li,

Zhang,

Deng

et al. 2024

Genes

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Manglietia Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study, we employed next-generation sequencing followed by de novo assembly to investigate the adaptive evolution of Manglietia using plastid genetic information. We newly sequenced the complete or nearly complete plastomes of four Manglietia species (Manglietia aromatica, Manglietia calcarea, Manglietia kwangtungensis, and Manglietia glauca) and conducted comparative analysis with seventeen published plastomes to examine the evolutionary pattern within this genus. The plastomes of these five newly sequenced Manglietia species range from 157,093 bp (M. calcarea2) to 160,493 bp (M. kwangtungensis), all exhibiting circular structures when mapped. Nucleotide diversity was observed across the plastomes, leading us to identify 13 mutational hotspot regions, comprising eight intergenic spacer regions and five gene regions. Our phylogenetic analyses based on 77 protein-coding genes generated phylogenetic relationships with high support and resolution for Manglietia. This genus can be divided into three clades, and the previously proposed infrageneric classifications are not supported by our studies. Furthermore, the close affinity between M. aromatica and M. calcarea is supported by the present work, and further studies are necessary to conclude the taxonomic treatment for the latter. These results provide resources for the comparative plastome, breeding, and plastid genetic engineering of Magnoliaceae and flowering plants.

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Towards comprehensive integration and curation of chloroplast genomes

Cited by 15 publications

References 12 publications

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Progress, challenge and prospect of plant plastome annotation

Comparative Analysis of Chloroplast Genomes for the Genus Manglietia Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution

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