Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid

Ng, Wei Lun; Wu, Wei; Zou, Peishan; Zhou, Renchao

doi:10.1093/aobpla/plz019

Cited by 7 publications

(10 citation statements)

References 79 publications

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“…The high-quality genome assembly of M. candidum makes it feasible to provide genomic insights into the evolution of trichomes, a key trait in contributing to species diversification and ecological adaptation in Melastoma (Wong, 2016;Ng et al, 2019;Huang et al unpublished data). Based on the remarkable trichome diversity in Melastoma, we predict the expansion of trichome-related genes in the M. candidum genome, which can provide the raw materials for trichome evolution and thus effective response to diverse biotic and abiotic stresses.…”

Section: Discussionmentioning

confidence: 99%

“…It also plays an important role in biological functions such as development, seed dispersal, adaptation to extreme temperatures, and signal transmission (Hegebarth et al, 2016;Zhao and Chen, 2016;Zhou et al, 2017). Previous studies in Melastoma suggested that trichomes of different species or populations might contribute to their differential adaptation to heterogenous habitats (Ng et al, 2019). For example, M. candidum, always found in open habitats, has densely covered scales in the hypanthia and densely covered hairs in the leaves, which can resist the (UV) irradiation.…”

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confidence: 99%

“…For example, M. candidum, always found in open habitats, has densely covered scales in the hypanthia and densely covered hairs in the leaves, which can resist the (UV) irradiation. In contrast, M. sanguineum usually occurs in shady understory, has sparse bristles in its hypanthia and glabrous leaves (Liu et al, 2014;Ng et al, 2019). In M. normale, populations with red and white trichomes in the young stems (twigs) exhibit higher fitness in their own habitats with high and low sunlight intensities, respectively, indicating differential adaptation 1 .…”

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confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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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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“…Oftentimes strategies employed follow two main paths. On one hand, de novo approaches are often used because they allow to represent the genes of both parental species (eg., [6,69]) but the gene structure in introns and exons (for species for which a reference is available) is then lost on the way, along with the information about the species each genes is representative of, in addition chimeric transcripts can also be assembled. On the other hand, some studies chose to use the genome of one of the two parents to conserve genome structure information and ease analyses but oftentimes the mapping rate of the other species is lower, and the analysis of gene expression in hybrids is biased toward one of the parental species (eg., [5]).…”

Section: Discussionmentioning

confidence: 99%

Schistosoma haematobiumandSchistosoma bovisfirst generation hybrids undergo large gene expressions remodeling consistent with species compatibility

Mathieu‐Bégné

Kincaid-Smith

Chaparro

et al. 2023

Preprint

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When two species hybridize, the two parental genomes are brought together and some alleles might interact for the first time. To the date, the extent of the transcriptomic changes in first hybrid generations, along with their functional outcome constitute an important knowledge gap especially in non-model organisms. Here we explored the molecular and functional outcomes of hybridization in first-generation hybrid between the blood fluke parasites S. haematobium and S. bovis. To this aim we fist assembled a hybrid reference transcriptome allowing us to measure gene expression in both parental species and hybrids to further described and quantified the profiles of gene expression encountered in hybrids. We identified large-scale gene expression remodeling since up to 55% of genes were differentially expressed in hybrids compared to at least one of the parental species. We further showed that intermediate level of expression in hybrids compared to parental species was the most prevalent expression profile (38% of genes) in agreement with S. haematobium x S. bovis high genomic compatibility and limited divergence. Also, among the differentially expressed genes of each of the identified profiles (intermediate, under-, over-expressed, or matching the expression of one of the parental species), only a few biological processes were found enriched without patterns being consistent through crosses and sexes. Our findings suggest that hybrid heterosis could be due to change in expression of a large portion of random genes which affect various biological processes.

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“…It has been reported that regulatory changes likely play a more important role than coding changes in closely related species of both animals and plants ( Jones et al, 2012 ; Ng et al, 2019 ). Lupa and BGE 016880 shared a high degree of similarity in their transcriptomes; however, gene expression levels in response to shade were quite different between them.…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative

Yuan

Caron²,

Vandenberg³

et al. 2022

Front. Genet.

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Lentil is an important pulse crop not only because of its high nutrient value but also because of its ecological advantage in a sustainable agricultural system. Our previous work showed that the cultivated lentil and wild lentil germplasm respond differently to light environments, especially to low R/FR-induced shade conditions. Little is known about how cultivated and wild lentils respond to shade at the level of gene expression and function. In this study, transcriptomic profiling of a cultivated lentil (Lupa, L. culinaris) and a wild lentil (BGE 016880, L. orientalis) at several growth stages is presented. De novo transcriptomes were assembled for both genotypes, and differential gene expression analysis and gene ontology enrichment analysis were performed. The transcriptomic resources generated in this study provide fundamental information regarding biological processes and genes associated with shade responses in lentils. BGE 016880 and Lupa shared a high similarity in their transcriptomes; however, differential gene expression profiles were not consistent between these two genotypes. The wild lentil BGE 016880 had more differentially expressed genes than the cultivated lentil Lupa. Upregulation of genes involved in gibberellin, brassinosteroid, and auxin synthesis and signaling pathways, as well as cell wall modification, in both genotypes explains their similarity in stem elongation response under the shade. Genes involved in jasmonic acid and flavonoid biosynthesis pathways were downregulated in BGE 016880 only, and biological processes involved in defense responses were significantly enriched in the wild lentil BGE 016880 only. Downregulation of WRKY and MYB transcription factors could contribute to the reduced defense response in BGE 016880 but not in Lupa under shade conditions. A better understanding of shade responses of pulse crop species and their wild relatives will play an important role in developing genetic strategies for crop improvement in response to changes in light environments.

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Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid

Cited by 7 publications

References 79 publications

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

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

Schistosoma haematobiumandSchistosoma bovisfirst generation hybrids undergo large gene expressions remodeling consistent with species compatibility

RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative

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