Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism

Pothiraj, Ramanujam; Ravikumar, Manohar Jebakumar; Backiyarani, S.; Uma, S.; Krishnamurthy, Panneerselvam

doi:10.1016/j.gene.2021.145472

Cited by 7 publications

(3 citation statements)

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“…The plant type III polyketide synthase (PKS) gene family, which catalyzes and synthesizes a variety of different structural and biologically active plant secondary metabolites, can provide unique polyketide backbones for various metabolic pathways (e.g., curcuminoids, flavonoids, stilbenes, diarylheptanoids and quinolones) associated with various functions of plant growth, development and defense ( Austin and Noel, 2003 ; Dao et al., 2011 ; Yu et al., 2012a ; Pothiraj et al., 2021 ). To further validate the subtype designation of C. longa PKSs, three species ( Z. officinale , M. acuminate , and O. sativa ) were selected for comparative analysis of PKS gene families.…”

Section: Resultsmentioning

confidence: 99%

“…We constructed a phylogenetic tree by aligning the PKS proteins among C. longa , Z. officinale , M. acuminate and O. sativa to confirm the classification of PKS family proteins in turmeric. The 30 turmeric PKS genes were clustered into four groups, the known chalcone synthases (CHSs), DCSs, CURSs and anther specific CHS (ASCs) ( Pothiraj et al., 2021 ) ( Figure 6A ). ASCs were specifically expressed in pollen development and comprise a monophyletic clade ( Ageez et al., 2005 ; Jiang et al., 2008 ).…”

Section: Resultsmentioning

confidence: 99%

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A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism

et al. 2022

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Curcuma longa, known as the ‘golden spice’ and ‘life spice’, is one of the most commonly utilized spices in the world and also has medicinal, cosmetic, dye and flavoring values. Herein, we present the chromosomal-level genome for turmeric to explore the differences between tubers and rhizomes in the regulation of curcumin biosynthesis and the mechanism of tuber formation. We assembled the turmeric genome into 21 pseudochromosomes using Pacbio long reads complemented with Hi-C technologies, which has a total length of 1.11 Gb with scaffold N50 of 50.12 Mb and contains 49,612 protein−coding genes. Genomic evolutionary analysis indicated that turmeric and ginger have shared a recent WGD event. Contraction analysis of gene families showed possible roles for transcription factors, phytohormone signaling, and plant-pathogen interactions associated genes in adaptation to harsh environments. Transcriptomic data from tubers at different developmental stages indicated that candidate genes related to phytohormone signaling and carbohydrate metabolic responses may be associated with the induction of tuber formation. The difference in curcumin content between rhizomes and tubers reflected the remodeling of secondary metabolites under environmental stress, which was associated with plant defense in response to abiotic stresses. Overall, the availability of the C. longa genome provides insight into tuber formation and curcumin biosynthesis in turmeric as well as facilitating the understanding of other Curcuma species.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism

et al. 2022

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“…They take part in various important biosynthesis of secondary metabolites related to polyketides, facilitate the production of various natural products [ 146 , 147 ], and play a role in defense responses and development [ 147–149 ]. In Musa , T3PKSs can initiate phenylphenalenone biosynthesis; phenylphenalenones are major phytoalexins involved in the defense against multiple pathogens in Musa [ 149 ]. The T3PKS BGCs in Musa merit further investigation because of their potential for enhancing defense systems.…”

Section: Discussionmentioning

confidence: 99%

Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

et al. 2022

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Background Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. Findings The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. Conclusions The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.

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Polyketides

Ziani

Mohamed

Ziani³

et al. 2023

Natural Secondary Metabolites

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Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism

Cited by 7 publications

References 61 publications

A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism

A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism

Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

Polyketides

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