Genome structure and evolution of Antirrhinum majus L

Ren

Molecular Ecology Resources

et al. 2020

Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid herbaceous plant with 26 chromosomes (2n = 26) and belongs to the family Cucurbitaceae. To address the limited knowledge of the genome of Luffa species, the chromosome‐level genome of L. cylindrica was assembled and analysed using PacBio long reads and Hi‐C data. We combined Hi‐C data with a draft genome assembly to generate chromosome‐length scaffolds. Thirteen scaffolds corresponding to the 13 chromosomes were assembled from 1,156 contigs to a final size of 669 Mb with a contig N50 size of 5 Mb and a scaffold N50 size of 53 Mb. After removing redundant sequences, 416.31 Mb (62.18% of the genome) of repeat sequences was detected. Subsequently, 31,661 protein‐coding genes with an average of 5.69 exons per gene were identified in the L. cylindrica genome using de novo methods, transcriptome data and homologue‐based approaches. In addition, 27,552 protein‐coding genes (87.02%) were annotated in five databases. According to the phylogenetic analysis, L. cylindrica is closely related to Cucurbita and Cucumis species and diverged from their common ancestor ~28.6–67.1 million years ago. Genome collinearity analysis was performed in Cucurbita moschata, Cucumis sativus and L. cylindrica, and it demonstrated a high degree of conserved gene order in these three species. The completeness of the genome will provide high‐quality genomic knowledge on breeding and reveal genetic variation in L. cylindrica.

Section: Resultsmentioning

confidence: 99%

“…phyml (version 3.0) with ‐type ml ‐d nt parameter settings were used for phylogenetic tree construction. The divergence time between L. cylindrica and other species was calculated by mcmctree (in paml version 4.4; M. Li et al, ).…”

Section: Methodsmentioning

confidence: 99%

Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

Ren

Molecular Ecology Resources

et al. 2020

“…The eluted proteins were digested with trypsin and the resulting peptides were recovered by solid-phase extraction followed by sequencing by LC-MS/MS. The peptides were identified by mapping the derived peptide sequences against the snapdragon genome sequence 36 .…”

Section: Methodsmentioning

confidence: 99%

A conserved strategy of chalcone isomerase-like protein to rectify promiscuous chalcone synthase specificity

et al. 2020

Land plants produce diverse flavonoids for growth, survival, and reproduction. Chalcone synthase is the first committed enzyme of the flavonoid biosynthetic pathway and catalyzes the production of 2′,4,4′,6′-tetrahydroxychalcone (THC). However, it also produces other polyketides, including p-coumaroyltriacetic acid lactone (CTAL), because of the derailment of the chalcone-producing pathway. This promiscuity of CHS catalysis adversely affects the efficiency of flavonoid biosynthesis, although it is also believed to have led to the evolution of stilbene synthase and p-coumaroyltriacetic acid synthase. In this study, we establish that chalcone isomerase-like proteins (CHILs), which are encoded by genes that are ubiquitous in land plant genomes, bind to CHS to enhance THC production and decrease CTAL formation, thereby rectifying the promiscuous CHS catalysis. This CHIL function has been confirmed in diverse land plant species, and represents a conserved strategy facilitating the efficient influx of substrates from the phenylpropanoid pathway to the flavonoid pathway.

“…Gene tandem duplication was one of the most intriguing features of the S. suberectus genome. Gene tandem duplication contributed to the development and environment adaption of different plants, such as the Leguminous plants nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes were duplicated to improve the tolerance to kinds of diseases in the soybean (Shao et al, 2014) and most TCP, cytochrome P450, and NB-ARC domain gene families were derived from tandem duplication events in the genome of Antirrhinum majus L. to affect the development of flowers and abiotic stress response (Li et al, 2019). With the high-quality genome sequence for S. suberectus, a series of flavonoid-related genes were identified in S. suberectus genome compared to model plants.…”

Section: Correspondence Analysis Between the Flavonoids Content And Tmentioning

confidence: 99%

Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis

et al. 2020

Spatholobus suberectus Dunn (S. suberectus), has been widely used in traditional medicines plant source of the Leguminosae family. Its vine stem of which plays an important role in the prevention and treatment of various diseases because it contains various flavonoids. Comparative genome analysis suggested well-conserved genomic components and genetic collinearity between the genome of S. suberectus and other genera of Leguminosae such as Glycine max. We discovered two whole genome duplications (WGD) events in S. suberectus and G. max lineage underwent a WGD after speciation from S. suberectus. The determination of expansion and contractions of orthologous gene families revealed 1,001 expanded gene families and 3,649 contracted gene families in the S. suberectus lineage. Comparing to the model plants, many novel flavonoid biosynthesis-related genes were predicted in the genome of S. suberectus, and the expression patterns of these genes in the roots are similar to those in the stems [such as the isoflavone synthase (IFS) genes]. The expansion of IFS from a single copy in the Leguminosae ancestor to four copies in S. suberectus, will accelerate the biosynthesis of flavonoids. MYB genes are widely involved in plant flavonoid biosynthesis and the most abundant member of the TF family in S. suberectus. Activated retrotransponson positive regulates the accumulation of flavonoid in S. suberectus by introducing the cis-elements of tissue-specific expressed MYBs. Our study not only provides significant insight into the evolution of specific flavonoid biosynthetic pathways in S. suberectus, but also would facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding for alleviating resource shortage of S. suberectus.