Mitochondrial genome of Garcinia mangostana L. variety Mesta

Wee, Ching-Ching; Muhammad, Nor Azlan Nor; Subbiah, Vijay Kumar; Arita, Masanori; Nakamura, Yasukazu; Goh, Hoe-Han

doi:10.1038/s41598-022-13706-z

Cited by 8 publications

(9 citation statements)

References 65 publications

(83 reference statements)

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“…4 a), and 16 pair medium sized repeats between 120 and 920 bp in the P. serratifolia mitogenome (Supplementary Table S5 ). The distribution of repeat is consistent with many plant mitogenomes that have one or more pairs of large repeats 38 , 42 , 43 . Some reports showed that larger and medium-sized repeats can act as sites for inter- or intramolecular recombination, leading to multiple alternative arrangements or isoforms 42 , 43 .…”

Section: Resultssupporting

confidence: 81%

“…5 , the sequencing reads coverage of these repeats is similar to those of other non-repetitive sequences, which implies no branching nodes in each repeat. Therefore, P. serratifolia mitochondrial master genome assembly can be represented in the circular form, as previously reported in plant mitogenomes 20 , 38 , 44 . However, there is a total length of 88,247 bp between the two copies of the long repeats (Fig.…”

Section: Resultsmentioning

confidence: 76%

“…The repetitive sequence in the P. serratifolia mitogenome was 51.05 kb, accounting for 10.78% of the mitogenome. The proportion of repeats is higher than that in Garcinia mangostana (5.8%) 38 and Prunus salicina (7.22%) 39 , but lower than that in Nicotiana tabacum (13%) 40 and Daucus carota (16%) 41 . The www.nature.com/scientificreports/ different proportions of repeats may be because the mitochondria of G. mangostana and P. salicina are mainly short repeating units, whereas those of P. serratifolia and D. carota are mainly longer repeating units 41 .…”

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confidence: 64%

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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Wang

Chen

et al. 2023

Sci Rep

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Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly and annotation of Photinia serratifolia, which is 473,579 bp in length, contains 38 protein-coding genes, 23 tRNAs, and 6 rRNAs, with 61 genes have no introns. The rps2 and rps11 genes are missing in the P. serratifolia mitogenome. Although there are more editing sites (488) in the P. serratifolia mitogenome than in most angiosperms, fewer editing types were found in the P. serratifolia mitogenome, showing a clear bias in RNA-editing. Phylogenetic analysis based on the mitogenomes of P. serratifolia and 8 other taxa of the Rosaceae family reflected the exact evolutionary and taxonomic status of P. serratifolia. However, Ka/Ks analysis revealed that 72.69% of the protein-coding genes in the P. serratifolia mitogenome had undergone negative selections, reflecting the importance of those genes in the P. serratifolia mitogenome. Collectively, these results will provide valuable information for the evolution of P. serratifolia and provide insight into the evolutionary relationships within Photinia and the Rosaceae family.

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Section: Resultssupporting

confidence: 81%

Section: Resultsmentioning

confidence: 76%

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confidence: 64%

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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Wang

Chen

et al. 2023

Sci Rep

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“…ACG was used as a start codon in nad1 gene of P. pedunculata mitochondria directly, possibly due to a C-to-U conversion at the second site without editing in mitogenome ( Zandueta-Criado and Bock, 2004 ). RNA editing events were reported existing in the initiation codon of nad1 in other plants ( Li et al., 2018 ; Fang et al., 2021 ; Wee et al., 2022 ). Consistent to most plants, there is few RNA editing events occur in rRNA, tRNA and introns ( Giegé and Brennicke, 1999 ).…”

Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Liu,

Wu,

Tian

et al. 2023

Front. Plant Sci.

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IntroductionPrunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.MethodsIn the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.Results and discussionThe P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

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“…In Malaysia, two varieties of G. mangostana (Manggis and Mesta) were sequenced and deposited to GenBank [ 16 , 17 , 18 ]. The mitogenome of the Mesta variety was reported recently [ 19 ]. However, a complete analysis of the plastomes from these two varieties is yet to be reported.…”

Section: Introductionmentioning

confidence: 99%

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species

Wee

Muhammad

Subbiah

et al. 2023

Plants

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The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

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Mitochondrial genome of Garcinia mangostana L. variety Mesta

Cited by 8 publications

References 65 publications

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species

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