The first mitochondrial genome of Melastoma dodecandrum resolved structure evolution in Melastomataceae and micro inversions from inner horizontal gene transfer

Zhou, Yuzhen; Zheng, Ruiyue; Peng, Yukun; Chen, Jiemin; Zhu, Xuanyi; Xie, Kai; Ahmad, Sagheer; Chen, Jinliao; Wang, Fei; Shen, Mingli; Luo, XianMei; Zhao, Kai; Peng, Donghui

doi:10.1016/j.indcrop.2023.117390

Cited by 4 publications

(3 citation statements)

References 30 publications

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“…Based on the analysis of the conserved domains of ARF, it was found that MedARF5B, MedARF6A, and MedARF9A possessed the PB1 domain. This suggests that the presence of the PB1 domain in these genes may lead to the formation of LLPS (liquid-liquid phase separation) condensates during their expression, thereby influencing the localization of ARF [26].…”

Section: Discussionmentioning

confidence: 99%

“…However, there has been limited research on the molecular mechanisms underlying the regulation of its growth and development. In recent years, the Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center at Fujian Agriculture and Forestry University has made significant progress in the assembly and annotation of M. dodecandrum's nuclear genome [25], mitochondrial genome [26], and chloroplast genome [27]. This progress has allowed us to gain valuable insights into the genetic makeup and organization of M. dodecandrum.…”

Section: Introductionmentioning

confidence: 99%

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A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

Peng,

Zhao,

Zheng

et al. 2024

IJMS

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Auxin Response Factors (ARFs) mediate auxin signaling and govern diverse biological processes. However, a comprehensive analysis of the ARF gene family and identification of their key regulatory functions have not been conducted in Melastoma dodecandrum, leading to a weak understanding of further use and development for this functional shrub. In this study, we successfully identified a total of 27 members of the ARF gene family in M. dodecandrum and classified them into Class I–III. Class II–III showed more significant gene duplication than Class I, especially for MedARF16s. According to the prediction of cis-regulatory elements, the AP2/ERF, BHLH, and bZIP transcription factor families may serve as regulatory factors controlling the transcriptional pre-initiation expression of MedARF. Analysis of miRNA editing sites reveals that miR160 may play a regulatory role in the post-transcriptional expression of MeARF. Expression profiles revealed that more than half of the MedARFs exhibited high expression levels in the stem compared to other organs. While there are some specific genes expressed only in flowers, it is noteworthy that MedARF16s, MedARF7A, and MedARF9B, which are highly expressed in stems, also demonstrate high expressions in other organs of M. dodecandrum. Further hormone treatment experiments revealed that these MedARFs were sensitive to auxin changes, with MedARF6C and MedARF7A showing significant and rapid changes in expression upon increasing exogenous auxin. In brief, our findings suggest a crucial role in regulating plant growth and development in M. dodecandrum by responding to changes in auxin. These results can provide a theoretical basis for future molecular breeding in Myrtaceae.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

Peng,

Zhao,

Zheng

et al. 2024

IJMS

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“…A pioneer species is a type of plant, fungus, or organism that is among the first to colonize or inhabit a newly formed or disturbed habitat [10]. As a pioneer plant, M. dodecandrum possesses typical advantages of pioneer species [11]. The stems of M. dodecandrum have numerous adventitious roots, which can help it adapt more easily to new habitats.…”

Section: Introductionmentioning

confidence: 99%

The Genome-Level Survey of the WOX Gene Family in Melastoma dodecandrum Lour.

Zheng,

Peng,

Chen

et al. 2023

IJMS

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Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Melastoma dodecandrum Lour., which shows pioneer position in land ecosystem formation and produces nutritional fruits. Identifying the WOX family genes in M. dodecandrum is imperative for elucidating its growth and development mechanisms. However, the WOX genes in M. dodecandrum have not yet been characterized. In this study, by identification 22 WOX genes in M. dodecandrum based on current genome data, we classified family genes into three clades and nine types with homeodomains. We highlighted gene duplications of MedWOX4, which offered evidences of whole-genome duplication events. Promoter analysis illustrated that cis-regulatory elements related to light and stress responses and plant growth were enriched. Expression pattern and RT-qPCR results demonstrated that the majority of WOX genes exhibited expression in the stem. MedWOX13s displayed highest expression across various tissues. MedWOX4s displayed a specific expression in the stem. Collectively, our study provided foundations for elucidating WOX gene functions and further molecular design breeding in M. dodecandrum.

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Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata ‘ZA’ and Other Species

Wang,

Zhang

et al. 2024

Biomolecules

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Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of ‘ZA’, a mutant type of M. baccata. In this study, we compared the differences between ‘ZA’ and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata ‘ZA’ was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata ‘ZA’, as well as interspecific variations among different individuals. In comparison, the total length of the ‘ZA’ mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the ‘ZA’ mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including ‘ZA’), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that ‘ZA’ is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.

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The first mitochondrial genome of Melastoma dodecandrum resolved structure evolution in Melastomataceae and micro inversions from inner horizontal gene transfer

Cited by 4 publications

References 30 publications

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

The Genome-Level Survey of the WOX Gene Family in Melastoma dodecandrum Lour.

Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata ‘ZA’ and Other Species

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