Factors contributing to mitogenome size variation and a recurrent intracellular DNA transfer in Melastoma

Zhou, Shuaixi; Zhi, Xueke; Yu, Runxian; Liu, Ying; Zhou, Renchao

doi:10.1186/s12864-023-09488-x

Cited by 3 publications

(2 citation statements)

References 75 publications

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“…Research on mitochondrial genomes have provided comprehensive insights into molecular evolution patterns, population dynamics, and adaptive processes across a wide array of organisms [1][2][3][4][5][6]. Mitochondrial genomes have been pivotal in molecular evolution and global genetic barcoding initiatives for species identification due to its small size, high substitution rate [7], lack of recombination and large copy number [8,9].…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

Alvarenga,

D’Elia,

Rocha

et al. 2024

BMC Genomics

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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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Section: Introductionmentioning

confidence: 99%

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

Alvarenga,

D’Elia,

Rocha

et al. 2024

BMC Genomics

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“…Plant mitogenomes exhibit diverse structures characterized by multiple rearrangements. In addition, IGTs and HGTs have been reported in plant mitogenomes, further complicating the prediction of their characteristics [19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids

Zhao,

Li,

Zhai

et al. 2024

IJMS

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Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.

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Mitogenome Assembly Reveals Gene Migration and RNA Editing Events in Plateau Hongliu (Myricaria elegans Royle.)

Li,

Wu,

et al. 2024

Forests

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The Plateau Hongliu (Myricaria elegans Royle.) is a woody shrub halophyte that thrives in arid areas of western Tibet, in the Himalayan Mountains. It is acclaimed as superior in saline stress acclimation and as a critical pharmaceutical resource of the Tibetan traditional herb. Nevertheless, the mitogenome in the genus Myricaria remains unknown. Here, using the Illumina and PacBio sequencing assays, the first complete mitogenome of the M. elegans revealed a multi-branched skeleton with a total length of 416,354 bp and GC content of 44.33%, comprising two circular molecules (M1 and 2). The complete mitogenome annotates 31 unique protein-encoding genes (PEGs), fifteen tRNAs, and three rRNA genes. The UAA exhibits the most prominent codon usage preference as a termination, followed by UUA codons for leucine. The mitogenome contains 99 simple sequence repeats and 353 pairs of dispersed repeats, displaying the most frequent in palindromic repeats. Gene transfer analyses identified 8438 bp of 18 homologous fragments from the plastome, accounting for 2.03% of the total length. Using the PREP suite, 350 C-U RNA editing sites were predicted, of which nad4 and ccmB were on the top frequency. Syntenic and phylogenetic analyses suggested weakly conserved patterns of M. elegans in Caryophyllales owing to the genome rearrangement. In summary, the deciphered unique features and complexities of the mitogenome in M. elegans provide novel insights into understanding the evolution and biological conservation underlying climate resilience in halophytes.

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Factors contributing to mitogenome size variation and a recurrent intracellular DNA transfer in Melastoma

Cited by 3 publications

References 75 publications

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids

Mitogenome Assembly Reveals Gene Migration and RNA Editing Events in Plateau Hongliu (Myricaria elegans Royle.)

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