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

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

doi:10.3390/plants12040930

Cited by 6 publications

(3 citation statements)

References 93 publications

(119 reference statements)

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“…Regarding the initiation codon of ndhD, ACG is commonly used as an alternative to AUG in many land plants, but it can still be converted to a functional AUG initiator codon by RNA editing [103][104][105], probably depending on a molecular cofactor PPR protein CRR4 during transcription [106]. Additionally, GUG is also reported as an initiation codon of psbC and rps19 in other plants, such as Thalictrum (Ranunculaceae) [105], Garcinia (Clusiaceae) [107], Populus (Salicaceae) [108] and Betula platyphylla (Betulaceae) [109], but these two genes cannot be edited back to AUG. However, recent studies suggested that an important translation initiation signal, known as Shine-Dalgarno (SD) sequence, can interact with 3' end of the 16S rRNA and facilitate translation initiation from the GUG [109,110], which is responsible for expression of psbC and rps19 in chloroplast.…”

Section: Discussionmentioning

confidence: 99%

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Niu

Lin

Tong

et al. 2023

Preprint

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Background Justicia is the largest genus in Acanthaceae and widely distributed in Asia, Africa, Australia and South America. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp) genomes of twelve Asian plants and combined with the previously published cp genome of J. leptostachya for further comparative genomics and phylogenetic analyses.Results All the cp genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434–83,676 bp), a small single copy (SSC, 16,833–17,507 bp) and two inverted repeats (IR, 24,947–25,549 bp). GC contents range from 38.1–38.4%. All the plastomes contain 114 genes, containing 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for Justicia phylogeny. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with morphology evolution of inflorescence position from terminal to axillary and spikes gradually shorten into cymes.Conclusion Our study not only elucidates basic features of Justicia whole plastomes, but also first sheds light on interspecific relationships of Asian Justicia plants.

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Section: Discussionmentioning

confidence: 99%

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Niu

Lin

Tong

et al. 2023

Preprint

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“…(e.g., salak) and Syzygyium spp. (e.g., java apple) (Blench, 2008; Larson et al, 2014; Lebot, 1999; Shaharudin et al, 2022; Thorogood et al, 2022; M. Wang et al, 2018; Warschefsky & von Wettberg, 2019; Wee et al, 2022; Wu, Terol, et al, 2018). Domestication of many of these fruit crops could reflect the pattern we have observed, whereby wild progenitors with small fruits were found in more mountainous areas and large fruit progenitors in the more productive wet lowlands.…”

Section: Discussionmentioning

confidence: 99%

Environment‐dependent influence of fruit size upon the distribution of the Malesian archipelagic flora

Trethowan¹,

Jennings²,

Bramley³

et al. 2022

Plants People Planet

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Societal Impact StatementWe found evidence that larger fruited plant species are more likely to be found in aseasonal wet areas of Malesia. These areas are likely to be impacted by increasing human encroachment, which threatens both large‐fruited species and the large fauna that are most likely responsible for their dispersal. This synergistic threat could drive the loss of fruit‐crop relatives that potentially have key traits for resilient fruit crops of the future.Summary It is unclear how fruit size determines distributions of megadiverse tropical flora. Energetic constraints of ecosystems suggest plant species with larger fruit should be found in the higher productivity, aseasonal wet tropics. However, the probability of seed dispersal over large scales should be increased by fruits being smaller, due to being available to a greater number of dispersal agents. We use a Bayesian phylogenetic model of species occurrence for >3400 species in Malesia to test how fruit size and environment interact to determine species distributions across the archipelago. We show that larger fruited species are more likely to occur in aseasonal wet areas. We also found that smaller fruit size was associated with species occurrence in more mountainous areas. Fruit size interacts with environmental variables to shape plant distributions across the megadiverse Malesian islands. The evolutionary processes that influence the patterns we have observed require further examination.

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“…borneensis , are genetically differentiated, or whether differences between them in morphological traits are due to phenotypic plasticity. Genome (Abu Bakar et al, 2016) and plastome (Wee et al, 2022) datasets of cultivated mangosteen are now available for reference for Single Nucleotide Polymorphism (SNP) calling. Analysis of both nrDNA and cpDNA markers in a large number of samples from across the region would enable inferences about several open questions: (i) patterns of genetic variation in mangosteen and its wild relatives; (ii) whether gene flow occurs between them, and whether any gene flow detected is unidirectional (from wild pollen donors to mangosteen), as expected from results of crossing experiments (Hambali & Natawijaya, 2016); (iii) whether mangosteen originated from numerous initial progenitors that arose from independent events of sexual reproduction.…”

Section: Synthesismentioning

confidence: 99%

The origin of cultivated mangosteen (Garcinia mangostana L. var. mangostana): Critical assessments and an evolutionary‐ecological perspective

Yao

Nazre

McKey

et al. 2023

Ecology and Evolution

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Mangosteen (Garcinia mangostana var. mangostana, Clusiaceae) is often dubbed the "Queen of Fruits" (Fairchild, 1915). The fruit has gained great fame for the exquisite taste of its snow-white flesh and is widely considered to be the finest fruit of the world (Almeyda & Martin, 1976;Dahlgren, 1947). A typical mangosteen fruit consists of usually six carpels, each with a segment of pulpy flesh, which collectively constitute the endocarp. Each segment encloses an ovule, but usually only one or two develop into seeds (asexually produced) in each fruit.Mangosteen is the only Garcinia L. taxon widely cultivated at commercial scale for its fruit and has been introduced throughout the humid tropics. Southeast Asia is the major production area of

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

Cited by 6 publications

References 93 publications

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Environment‐dependent influence of fruit size upon the distribution of the Malesian archipelagic flora

The origin of cultivated mangosteen (Garcinia mangostana L. var. mangostana): Critical assessments and an evolutionary‐ecological perspective

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