Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics

Ke, Shijie; Liu, Ding-Kun; Tu, Xiong-De; He, Xin; Zhang, Mengmeng; Zhu, Mengjia; Zhang, Diyang; Zhang, Cuili; Lan, Siren; Liu, Zhong‐Jian

doi:10.3390/ijms24097837

Cited by 15 publications

(7 citation statements)

References 65 publications

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“…Codon usage was generally strongly biased toward A or T (U) at the third codon position in the P. granatum mitogenome. Similar results had been found in the mitogenome of other plants [ 17 , 27 ].…”

Section: Resultssupporting

confidence: 88%

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

Feng,

Wang,

Wang

et al. 2023

BMC Plant Biol

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Background Punica granatum is a fundamentally important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study the P. granatum mitogenome was sequenced and assembled to further understanding of organization, variation, and evolution of mitogenomes of this tree species. Results The genome structure was multi-chromosomes with seven circular contigs, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths of 30 or greater, primarily consisting of reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum ‘Taishanhong’ was closely related to P. granatum ‘Qingpitian’ and Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship. Conclusion The results offered crucial information on the evolutionary biology of pomegranate and highlighted ways to promote the utilization of the species’ germplasm.

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Section: Resultssupporting

confidence: 88%

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

Feng,

Wang,

Wang

et al. 2023

BMC Plant Biol

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Section: Condon Usage and Rscu Analysissupporting

confidence: 88%

Multichromosomal Mitochondrial Genome of Punica granatum: Comparative Evolutionary Analysis and Gene Transformation from chloroplast genomes

Feng

Wang

Yang

et al. 2023

Preprint

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Background Punica granatum is an essentially important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. To further understand the organization, variation, and evolution of pomegranate mitogenomes, the P. granatum mitogenome was sequenced and assembled in the study. Results The genome structure was multi-chromosomes with seven circular chromosomes, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum was closely related to Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship. Conclusion The results provided the predominant information for pomegranate evolutionary biology and to promote the species germplasm utilization.

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“…In recent years, the swift advancement of DNA sequencing technology has led to an accumulation of substantial data for phylogenetic research 4 . Scientists have extracted a series of different types of phylogenetic signals from the genome, such as SNPs, low-copy genes, and small genomes like chloroplasts, mitochondrial genomes 5 , and viral genomes. To delineate the phylogenetic relationships of different taxa, it is essential to integrate vast amounts of data and various types of phylogenetic data due to the differences in evolutionary scales.…”

Section: Introductionsmentioning

confidence: 99%

PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals

Wang,

Dong,

Liang

et al. 2024

Preprint

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With the explosive growth of biological data, the dimensions of phylogenetic research have expanded to encompass various aspects, including the study of large-scale populations at the microevolutionary level and comparisons between different species or taxonomic units at the macroevolutionary level. Traditional phylogenetic tools often struggle to handle the diverse and complex data required for these different evolutionary scales. In response to this challenge, we introduce PhyloForge-a robust tool designed to seamlessly integrate the demands of both micro- and macro-evolution, comprehensively utilizing diverse phylogenomic signals, such as genes, SNPs, structural variations, as well as mitochondrial and chloroplast genomes. PhyloForge's groundbreaking innovation lies in its capability to seamlessly integrate multiple phylogenomic signals, enabling unified analysis of multidimensional genomic data. This unique feature empowers researchers to gain a more comprehensive understanding of diverse aspects of biological evolution. PhyloForge not only provides highly customizable analysis tools for experienced researchers but also features an intuitively designed interface, facilitating effortless phylogenetic analysis for beginners. Extensive testing across various domains, including animals, plants, and fungi, attests to its broad applicability in the field of phylogenetics. In summary, the developmental background and innovative features of PhyloForge position it with significant potential in the era of large-scale genomics, offering a new perspective and toolset for a deeper understanding of the evolution of life.

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Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics

Cited by 15 publications

References 65 publications

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

Multichromosomal Mitochondrial Genome of Punica granatum: Comparative Evolutionary Analysis and Gene Transformation from chloroplast genomes

PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals

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