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The complete mitochondrial genome of Luffa acutangula.

ABSTRACT: Based on PacBio de novo assembly, we report the first complete mitochondrial genome of Luffa acutangula (460,333 bp) containing nine large chloroplast-derived sequences (1.9-17.3 kb) across the mitogenome. The base composition of the mitogenome in descending order is A: 28.02%, C: 22.04%, G: 21.83% and T: 28.10%, and the G + C content is 43.87%. There are 63 mitochondrial genes including 40 protein-coding genes, 3 rRNA genes and 20 tRNA genes. Additionally, a total of 288 repeats ranging from 31 to 5,301 bp were identified, accounting for 5.7% of the mitogenome. Two large direct repeats (5,301 and 405 bp) within the mitogenome were found for the formation of four subgenomic molecules. A phylogenetic analysis showed that L. acutangula was closely related to other species in Cucurbiaceae. This mitogenome provides useful genetic information for evolutionary studies.

SUBMITTER: Ruang-Areerate P

PROVIDER: S-EPMC7781975 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Chloroplast genome data of Luffa acutangula and Luffa aegyptiaca and their phylogenetic relationships.

Project description:Luffa acutangula and Luffa aegyptiaca are domesticated plants in the family Cucurbitaceae. They are mainly cultivated in the tropical and subtropical regions of Asia. The chloroplast genomes of many Cucurbitaceae species were sequenced to examine gene content and evolution. However, the chloroplast genome sequences of L. acutangula and L. aegyptiaca have not been reported. We report the first complete sequences of L. acutangula and L. aegyptiaca chloroplast genomes obtained from Pacific Biosciences sequencing and use them to infer evolutionary relationships. The chloroplast genomes of L. acutangula and L. aegyptiaca are 157,202 and 157,275 bp, respectively. Both genomes possessed the typical quadripartite structure and contained 131 genes, including 87 coding genes, 36 tRNA genes and 8 rRNA genes. We identified simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) from both chloroplast genomes. Polycistronic mRNA was examined in L. acutangula and L. aegyptiaca using RNA sequences from Isoform sequencing to identify co-transcribed genes. IR size and locations were compared to other species and found to be relatively unchanged. Phylogenetic analysis confirmed the close relationship between L. acutangula and L. aegyptiaca in the Cucurbitaceae lineage and showed separation of the Luffa monophyletic clade from other species in the subtribe Sicyocae. The results obtained from this study can be useful for studying the evolution of Cucurbitaceae plants.

| S-EPMC7644877 | biostudies-literature

Luffa acutangula

Project description:Luffa acutangula overview

| PRJNA812298 | ENA

Luffa acutangula

Project description:Luffa acutangula Raw sequence reads

| PRJNA606857 | ENA

Luffa acutangula

Project description:Luffa acutangula Genome sequencing and assembly

| PRJNA1042866 | ENA

Luffa acutangula

Project description:Luffa acutangula Transcriptome

| PRJNA810936 | ENA

Metabolome and Transcriptome Analyses of Cucurbitacin Biosynthesis in Luffa (Luffa acutangula).

Project description:Cucurbitacins are extremely bitter compounds mainly present in Cucurbitaceae, where Luffa belongs. However, there is no comprehensive analysis of cucurbitacin biosynthesis in Luffa fruit. Therefore, this study analyzed bitter (WM709) and non-bitter (S1174) genotypes of Luffa to reveal the underlying mechanism of cucurbitacin biosynthesis by integrating metabolome and transcriptome analyses. A total of 422 metabolites were detected, including vitamins, essential amino acids, antioxidants, and antitumor substances. Of these, 131 metabolites showed significant differences between bitter (WM709) and non-bitter (S1174) Luffa fruits. The levels of isocucurbitacin B, cucurbitacin D, 23,24-dihydro cucurbitacin E, cucurbitacin F were significantly higher in bitter than in non-bitter Luffa. Transcriptome analysis showed that Bi, cytochromes P450s (CYP450s), and acyltransferase (ACT) of the cucurbitacin biosynthesis pathway, were significantly up-regulated. Moreover, drought stress and abscisic acid (ABA) activated genes of the cucurbitacin biosynthesis pathway. Furthermore, dual-luciferase reporter and yeast one-hybrid assays demonstrated that ABA-response element binding factor 1 (AREB1) binds to the Bi promoter to activate Bi expression. Comparative analysis of the Luffa and cucumber genomes showed that Bi, CYP450s, and ACT are located in the conserved syntenic loci, and formed a cucurbitacin biosynthesis cluster. This study provides important insights into major genes and metabolites of the cucurbitacin biosynthetic pathway, deepening the understanding of regulatory mechanisms of cucurbitacin biosynthesis in Luffa.

| S-EPMC9209774 | biostudies-literature

In silico analysis of peroxidase from Luffa acutangula.

Project description:Peroxidases are oxidoreductase enzymes that widely gained attention as biocatalysts for their robust catalytic activity, specificity, and regioselective functionality for phenolic compounds. The study of molecular aspects of peroxidases is as crucial as that of the physicochemical aspects. A bioinformatics approach is utilized in this study to investigate the structural aspects and functions of luffa peroxidase (LPrx) from Luffa acutangula. The evolutionary relationship of LPrx with other class III peroxidases was studied by constructing a neighbour-joining phylogenetic tree. An analysis of the phylogenetic tree revealed that plant peroxidases share a common ancestor. The gene ontology term showed that LPrx had a molecular functionality of the oxidation-reduction process, heme binding and peroxidase-like activity, and the biological function of hydrogen peroxide scavenging activity. The enzyme-ligand interactions were studied from a catalytic point of view using the molecular docking technique. The molecular docking was carried out with LPrx as a receptor and guaiacol, m-cresol, p-cresol, catechol, quinol, pyrogallol, 2,4-dimethoxyphenol, gallic acid, aniline, and o-phenylenediamine as ligands. The results presented in the current communication will have a significant implication in proteomics, biochemistry, biotechnology, and the potential applications of peroxidases in the biotransformations of organic compounds.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-022-03432-8.

| S-EPMC9789927 | biostudies-literature

Draft Genome Sequence of Bacillus sp. Strain EKM601B (Phylum Firmicutes), Living inside the Seeds of Luffa acutangula (Chinese Okra).

Project description:Presented here is the draft genome sequence of Bacillus sp. strain EKM601B, which contains 4,199,360 bp in 73 contigs. This candidate endophyte was isolated from surface-sterilized dry seeds of Luffa acutangula (Chinese okra) and demonstrated diverse plant-beneficial functions and antagonism against soilborne pathogens in vitro.

| S-EPMC7225529 | biostudies-literature

A SNP of betaine aldehyde dehydrogenase (BADH) enhances an aroma (2-acetyl-1-pyrroline) in sponge gourd (Luffa cylindrica) and ridge gourd (Luffa acutangula).

Project description:Luffa is a genus of tropical and subtropical vines belonging to the Cucurbitaceae family. Sponge gourd (Luffa cylindrica) and ridge gourd (Luffa acutangula) are two important species of the genus Luffa and are good sources of human nutrition and herbal medicines. As a vegetable, aromatic luffa is more preferred by consumers than nonaromatic luffa. While the aroma trait is present in the sponge gourd, the trait is not present in the ridge gourd. In this study, we identified Luffa cylindrica's betaine aldehyde dehydrogenase (LcBADH) as a gene associated with aroma in the sponge gourd based on a de novo assembly of public transcriptome data. A single nucleotide polymorphism (SNP: A > G) was identified in exon 5 of LcBADH, causing an amino acid change from tyrosine to cysteine at position 163, which is important for the formation of the substrate binding pocket of the BADH enzyme. Based on the identified SNP, a TaqMan marker, named AroLuff, was developed and validated in 370 F2 progenies of the sponge gourd. The marker genotypes were perfectly associated with the aroma phenotypes, and the segregation ratios supported Mendelian's simple recessive inheritance. In addition, we demonstrated the use of the AroLuff marker in the introgression of LcBADH from the aromatic sponge gourd to the ridge gourd to improve aroma through interspecific hybridization. The marker proved to be useful in improving the aroma characteristics of both Luffa species.

| S-EPMC8904516 | biostudies-literature

A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula).

Project description:Key messageA dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

| S-EPMC8440308 | biostudies-literature

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