The Melastoma dodecandrum genome and the evolution of Myrtales

Yang, Hao; Zhou, Yuzhen; Chen, Bin; Chen, Gui-Zhen; Wen, Zhenying; Zhang, Diyang; Sun, Weihong; Liu, Ding-Kun; Huang, Jie; Chen, Jinliao; Xiao-qin, Zhou; Fan, Wanlin; Zhang, Wen-Chun; Luo, Lin; Han, Wenchao; Zheng, Yan; Li, Long; Lu, Pengcheng; Xing, Yue; Liu, Shuya; Sun, Jiating; Cao, Yinghui; Zhang, Yanping; Shi, Xiao-Ling; Wu, Shasha; Ai, Ye; Zhai, Jun-Wen; Lan, Siren; Liu, Zhong‐Jian; Peng, Donghui

doi:10.1016/j.jgg.2021.10.004

Cited by 18 publications

(36 citation statements)

References 71 publications

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“…Within rosids, the main conflicts with previous phylogenetic analyses related to the position of Myrtales and the phylogenetic relationships within clade II. Our results indicated that Myrtales are sister to other rosids, which is consistent with most analyses [37,[45][46][47][48][49][50][51][52][53]56] but not with an analysis of 1000 transcriptomes that suggests that Myrtales are nested within other malvids [27]. Within rosid clade II, our results support the hypothesis that Fagales are sister to the other species and Cucurbitales are sister to Fabales, whereas previous studies have concluded that Fagales and Fabales cluster together and Cucurbitales and Rosales are sister clades [27,43,50].…”

Section: Phylogenetic Relationship Between Buxales and Other Eudicot ...supporting

confidence: 90%

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

et al. 2022

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Background Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. Results Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. Conclusions Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.

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Section: Phylogenetic Relationship Between Buxales and Other Eudicot ...supporting

confidence: 90%

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

et al. 2022

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“…The topology of the constructed maximum likelihood tree of 13 species including M. candidum based on sequences of 346 single copy genes is consistent with previous studies (Myburg et al, 2014;Hao et al, 2022) and confirms that Myrtales is sister to the ancestor of Fabids and non-Myrtales Malvids (Figure 3), but is not consistent with its position shown in APGIV (2016). Melastoma is sister to Osbeckia, which is in agreement with previous studies (Veranso-Libalah et al, 2017).…”

Section: Phylogenetic Position and Short Species Diversification Hist...supporting

confidence: 81%

“…This implies that the two WGDs, the recent s event at Ks = 0.256-0.280 and the more ancient r event at Ks = 0.927-1.022, were shared by the three species. Both of the two WGDs occurred after diverging from Eucalyptus (Hao et al, 2022). Because the g triplication event is shared by all the core eudicots (Jiao et al, 2012), including Eucalyptus (Myburg et al, 2014), the two WGDs, both with smaller Ks peak values, must have happened after the g event.…”

Section: Genomic Synteny Between M Candidum and M Dodecandrummentioning

confidence: 98%

“…Based on the remarkable trichome diversity in Melastoma, we predict that trichome-related genes might have been expanded in the genome of this genus. To date, only the genome of M. dodecandrum has been reported (Hao et al, 2022), however, the annotation of this genome is not complete (see Results) and no analyses on trichome evolution have been performed in that study. Here we report the sequencing, assembly, annotation and characterization of the genome of M. candidum, an erect-growing species widely distributed in southern China, northern Vietnam and Okinawa of Japan (Chen, 1984).…”

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Chromosomal-level genome assembly of Melastoma candidum provides insights into trichome evolution

Zhong¹,

Wu²,

Sun³

et al. 2023

Front. Plant Sci.

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Melastoma, consisting of ~100 species diversified in tropical Asia and Oceania in the past 1-2 million years, represents an excellent example of rapid speciation in flowering plants. Trichomes on hypanthia, twigs and leaves vary markedly among species of this genus and are the most important diagnostic traits for species identification. These traits also play critical roles in contributing to differential adaptation of these species to their own habitats. Here we sequenced the genome of M. candidum, a common, erect-growing species from southern China, with the aim to provide genomic insights into trichome evolution in this genus. We generated a high-quality, chromosome-level genome assembly of M. candidum, with the genome size of 256.2 Mb and protein-coding gene number of 40,938. The gene families specific to, and significantly expanded in Melastoma are enriched for GO terms related to trichome initiation and differentiation. We provide evidence that Melastoma and its sister genus Osbeckia have undergone two whole genome duplications (WGDs) after the triplication event (γ) shared by all core eudicots. Preferential retention of trichome development-related transcription factor genes such as C2H2, bHLH, HD-ZIP, WRKY, and MYB after both WGDs might provide raw materials for trichome evolution and thus contribute to rapid species diversification in Melastoma. Our study provides candidate transcription factor genes related to trichome evolution in Melastoma, which can be used to evolutionary and functional studies of trichome diversification among species of this genus.

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“…Tender leaf, tender root, tender stem, small fruit, medium fruit, big fruit, flower bud, medium flower bud, and mature flower of wild M. dodecandrum were sampled for qPCR. The genome, transcriptome data, and GFF file used in this study follow Hao et al [ 41 ]. Hisat [ 42 ] and Stringtie2 [ 43 ] were used to align and assemble the transcriptome data of M. dodecandrum .…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

Huang

Chen

Ahmad

et al. 2023

IJMS

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Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family.

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The Melastoma dodecandrum genome and the evolution of Myrtales

Cited by 18 publications

References 71 publications

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

Chromosomal-level genome assembly of Melastoma candidum provides insights into trichome evolution

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

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