Plant organellar genomes: much done, much more to do

Wang, Jie; Kan, Shenglong; Liao, Xuezhu; Zhou, Jiawei; Tembrock, Luke R.; Daniell, Henry; Jin, Shuangxia; Wu, Zhiqiang

doi:10.1016/j.tplants.2023.12.014

Cited by 19 publications

(15 citation statements)

References 123 publications

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“…Mitochondrial generate energy through aerobic respiration in eukaryotic cells and play a key role in regulating important cellular activities such as differentiation, apoptosis, growth, and division 56,57 . Despite their similar functions, the Mitochondrial genomes of different plants exhibit significant differences in size and structure due to the presence of multiple types of repeat sequences and relatively conserved coding sequences, adding to their mystery with linear, fragmented, circular, branched, and multipartite structures 5,17,58,59 . In this study, we combined Illumina and PacBio sequencing technologies to first describe the basic characteristics of the P. frutescens genome.…”

Section: Discussionmentioning

confidence: 99%

“…In the mitogenome of P. frutescens, a total of 77 SSRs have been identified (Figure 2C). Among these SSRs, tetrameric repeats dominate, accounting for 27.35% (27) of the total count, followed by dimeric repeats (20), monomeric repeats (11), trimeric repeats (9), pentameric repeats (6), and hexameric repeats (5). Within the monomeric SSRs, adenine (A) repeats have the highest proportion (90.91%), and AG repeats have the highest proportion among dimeric repeats (65.00%) (Figure 2D).…”

Section: Repeat Sequence Analysismentioning

confidence: 99%

“…However, research on complete plant Mitochondrial genomes lags far behind that of complete plastid genomes. While there are nearly 13,000 complete plastid genomes in the NCBI database, there are only 673 complete plant Mitochondrial genomes 5 . This is due to the complex structure of plant Mitochondrial, which are difficult to purify and are frequently interfered with by chloroplasts and other organelles, making their genome assembly challenging.…”

Section: Introductionmentioning

confidence: 99%

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Complete mitochondrial genome of Perilla frutescens (Lamiaceae) insights into structure, Codon usage, repeats, and RNA editing

Wang,

Luo,

Lan

et al. 2024

Preprint

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Perilla frutescens (L.) Britton, a member of the Lamiaceae family, is a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in α-linolenic acid, holding significant economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete Mitochondrial genome sequence has yet to be reported. In this investigation, we conducted the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens using a combination of Illumina and PacBio data. The resulting assembled P. frutescens Mitochondrial genome spans 299,551 bp and exhibits a typical circular structure, with a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes, with 18 introns present in 8 protein-coding genes. Notably, the codons of the P. frutescens Mitochondrial genome display a notable A/T bias. Our analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Additionally, RNA editing sites exhibited a preference for the formation of leucine at amino acid editing sites. Furthermore, we identified 70 sequence fragments (12,680 bp) that have been transferred from the chloroplast to the Mitochondrial genome, accounting for 4.23% of the entire Mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense. Inter-species Ka/Ks results suggested that Ka/Ks <1 for 28 PCGs, indicating that these genes will continue to evolve under purifying selection pressure. The findings of this study will contribute to the enrichment of Mitochondrial genome data for P. frutescens and provide a theoretical foundation for future molecular breeding research on P. frutescens.

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Section: Discussionmentioning

confidence: 99%

Section: Repeat Sequence Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Complete mitochondrial genome of Perilla frutescens (Lamiaceae) insights into structure, Codon usage, repeats, and RNA editing

Wang,

Luo,

Lan

et al. 2024

Preprint

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“…Research on A. dahurica has predominantly concentrated on its biology, cultivation methods, chemical composition, and pharmacological properties. Yet, there remains a significant gap in the exploration of its genetic information ( Wang et al., 2024 ).…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, these rearrangements play a crucial role in the regulation of gene expression and mitochondrial function, underscoring the importance of understanding mitochondrial genome architecture in plant biology and breeding strategies ( Yang et al., 2022 ). More graph-based assembly tools have been published, including GSAT and PMAT ( He et al., 2023 ; Wang et al., 2024 ).…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae

Li,

Liu,

Zeng

et al. 2024

Front. Plant Sci.

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Angelica dahurica is a kind of Chinese traditional herbs with economic and ornament value, widely distributed in China. Despite its significance, there have been limited comprehensive investigations on the genome of A. dahurica, particularly regarding mitochondrial genomes. To investigate the conversion between mitochondrial genome and chloroplast genome, a complete and circular mitochondrial genome was assembled using Oxford Nanopore Technologies (ONT) long reads. The mitochondrial genome of A. dahurica had a length of 228,315 base pairs (bp) with 45.06% GC content. The mitochondrial genome encodes 56 genes, including 34 protein-coding genes, 19 tRNA genes and 3 rRNA genes. Moreover, we discovered that 9 homologous large fragments between chloroplast genome and mitochondrial genome based on sequence similarity. This is the first report for A. dahurica mitochondrial genome, which could provide an insight for communication between plastid genome, and also give a reference genome for medicinal plants within the Angelica family.

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