The complete chloroplast genome sequence of Amomum villosum Lour.
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ABSTRACT:
SUBMITTER: Ma M
PROVIDER: S-EPMC7748462 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The first complete chloroplast genome of Amomum villosum (Zingiberaceae) was reported in this study. The A. villosum genome was 163,608 bp in length, and comprised a pair of inverted repeat (IR) regions of 29,820 bp each, a large single-copy (LSC) region of 88,680 bp, and a small single-copy (SSC) region of 15,288 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The overall AT content was 63.92%. Phylogenetic analysis showed that A. villosum was closely related to two species Amomum kravanh and Amomum compactum within the genus Amomum in family Zingiberaceae.
| S-EPMC7706907 | biostudies-literature
Project description:ObjectiveAmomum villosum (AV) is an herb whose dried fruit has been extensively used in modern medicine to treat digestive system diseases such as dysentery, vomiting and abdominal pain. This paper aims to supplement chloroplast (cp) genomic resources and to be used in phylogenetic studies and identification of AV related plants.MethodsHigh-throughput sequencing technology was used to determine the complete sequence of the AV cp genome, and the sequence was then compared with three related species.ResultsThe genome size of AV we obtained was 163,968 bp with an obvious tetrad structure. The AV cp genome was observed to contain 125 unique genes and 81 simple sequence repeat (SSRs) had been determined and the majority of which were adenine-thymine (AT)-rich. Comparative analysis of genome sequence of four ginger plants showed that the atpF, clpP and rpl32 genes are potential markers for identifying Amomum species. Phylogenetic analysis suggested that AV was closely related to A. kravanh and A. compactum.ConclusionThese results have brought useful genetic resources for further identification researches, DNA barcoding, resolving taxonomy and understanding the evolutionary mode of Zingiberaceae cp genome.
| S-EPMC9476707 | biostudies-literature
Project description:ObjectiveTo explore the influence of biological characteristics on the yield of Amomum villosum Lour. and Amomum longiligulare T. L. Wu, to find an effective pollen viability evaluation method and storage method to solve the problem of the low yield of Amomum plants.MethodsFive germplasm of Amomum plants were used to investigate the effects of the phenological phase, pollen viability, and stigma receptivity on natural and artificial fruit set.ResultsAmomum longiligulare T. L. Wu showed late flowering, and its natural pollination rate is higher than that of Amomum villosum Lour. In all germplasm, the artificial pollination rate and fruit setting rate are more than 3 times higher than that under natural conditions. Fruits begin to drop seven days after successful pollination, and the fruit drop is basically stable after one month. The hybridization verification showed that TTC method was simpler and more accurate than in vitro germination method. Optimal storage conditions for pollen are 4°C and high humidity. After 36 h of storage, pollen can still be used for artificial cross-pollination or as hybrid parents.ConclusionThe special biological characteristics are the fundamental reason for the low natural pollination rate of Amomum plants. The accurate measurement method of Amomum plants pollen is the TTC method, and storage at 4°C and high humidity can increase the yield, which was six times that of the natural yield.
| S-EPMC8376005 | biostudies-literature
Project description:Amomum villosum Lour. (A. villosum) is a valuable herbaceous plant that produces the famous traditional Chinese medicine Amori Fructus. Identifying molecular markers associated with the growth of A. villosum can facilitate molecular marker-assisted breeding of the plant. This study employed 75 A. villosum accessions as the test material and utilized 71 pairs of polymorphic simple sequence repeat (SSR) molecular markers to genotype the population. The study analyzed the association between SSR markers and phenotypic traits through the linkage imbalance and population structure analysis. Candidate genes associated with the molecular markers were also identified. The results showed that the phenotypic diversity index range of the 12 agronomic traits was 4.081-4.312 and conformed to a normal distribution. Moreover, 293 allelic variations were detected in the 75 accessions, with an average of 5.32 amplified alleles per loci, ranging from 3 to 8. The maximum number of amplified alleles for AVL12 was 8. The population structure and cluster analysis indicated that the accessions could be divided into two subgroups. Using the mixed linear model (MLM) model of population structure (Q)+kinship matrix (K) for association analysis, three SSR molecular markers significantly associated with the agronomic traits were detected. Fluorescence quantification was used to analyze the expression levels of six candidate genes, and it was found that three of the genes were differentially expressed in phenotypically different accessions. This study is the first to use SSR markers for genome-wide association study (GWAS) mapping and identification of the associated agronomic traits in A. villosum. The results of this study provide a basis for identifying genetic markers for growth traits for marker-assisted breeding in A. villosum.
| S-EPMC11299815 | biostudies-literature
Project description:Amomum villosum Lour., produced from Yangchun, Guangdong Province, China, is a Daodi medicinal material of Amomi Fructus in traditional Chinese medicine. This herb germplasm should be accurately identified and collected to ensure its quality and safety in medication. In the present study, single nucleotide polymorphism typing method was evaluated on the basis of DNA barcoding markers to identify the germplasm of Amomi Fructus. Genomic DNA was extracted from the leaves of 29 landraces representing three Amomum species (A. villosum Lour., A. xanthioides Wall. ex Baker and A. longiligulare T. L. Wu) by using the CTAB method. Six barcoding markers (ITS, ITS2, LSU D1-D3, matK, rbcL and trnH-psbA) were PCR amplified and sequenced; SNP typing and phylogenetic analysis were performed to differentiate the landraces. Results showed that high-quality bidirectional sequences were acquired for five candidate regions (ITS, ITS2, LSU D1-D3, matK, and rbcL) except trnH-psbA. Three ribosomal regions, namely, ITS, ITS2, and LSU D1-D3, contained more SNP genotypes (STs) than the plastid genes rbcL and matK. In the 29 specimens, 19 STs were detected from the combination of four regions (ITS, LSU D1-D3, rbcL, and matK). Phylogenetic analysis results further revealed two clades. Minimum-spanning tree demonstrated the existence of two main groups: group I was consisting of 9 STs (ST1-8 and ST11) of A. villosum Lour., and group II was composed of 3 STs (ST16-18) of A. longiligulare T.L. Wu. Our results suggested that ITS and LSU D1-D3 should be incorporated with the core barcodes rbcL and matK. The four combined regions could be used as a multiregional DNA barcode to precisely differentiate the Amomi Fructus landraces in different producing areas.
| S-EPMC4274006 | biostudies-literature
Project description:Amomum kravanh is an important edible and medicinal herb, the dried fruits of which are widely used in traditional herbal medicine as cardamom. We sequenced and analyzed the complete chloroplast (cp) genome of A. kravanh with herbgenomics technologies. The size of the A. kravanh cp genome was 162,766 bp, which consisted of long (LSC; 87,728 bp) and short (SSC; 15,390 bp) single-copy regions, separated by a pair of inverted repeats (IRs; 29,824 bp). The genome encoded 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. A total of 299 simple sequence repeats (SSRs) were identified in the A. kravanh cp genome, which provides an effective method to study species identification and population genetics of the medicinal plant. Moreover, one complement, 12 forward, 12 palindrome and two reverse repeats were detected. Comparative cp genome sequence analysis of four Zingiberaceae species indicated that their intergenic spacers are highly divergent, although the gene order, gene content and genome structure differed only minimally. In particular, there was a remarkable expansion of the IR regions in the A. kravanh cp genome. Phylogenetic analysis strongly supported a sister relationship between A. kravanh and Alpinia zerumbet. This study identified the unique characteristics of the A. kravanh cp genome and might provide valuable information for future studies aiming for Amomum identification, and provide insights into the taxonomy of the commelinids.
| S-EPMC6150383 | biostudies-literature
Project description:Dioscorea esculenta (Lour.) Burkill is an essential tuber crop with pharmacological effects in the family Dioscoreaceae. The complete chloroplast genome of D. esculenta was determined in this study. The total genome size is 153, 437 bp in length and demonstrates a typical quadripartite structure containing a large single copy (LSC, 83,628 bp) and a small single copy (SSC, 18,893 bp), separated by a pair of inverted repeats (IRa, IRb) of 25,458 bp. The GC content of the complete chloroplast genome sequence is 37.07%. A total of 131 genes were predicted including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree analysis of 25 species belonging to the genus Dioscorea indicated that D. esculenta and D. sansibarensis were clustered into one branch.
| S-EPMC7703703 | biostudies-literature
Project description:Styrax agrestis (Lour.) G. Don, is a deciduous species of Styracaceae with beautiful shape, drooping flowers, and blooming like snow. Here, we characterized the complete chloroplast (cp) genome of S. agrestis using next generation sequencing. The circular complete cp genome of S. agrestis is 157,893 bp in length, containing a large single-copy (LSC) region of 87,512 bp, and a small single-copy (SSC) region of 18,285 bp. It comprises 136 genes, including eight rRNA genes, 37 tRNAs genes, 90 protein-coding genes, and one pseudo gene. The GC content of S. agrestis cp genome is 36.96%. The phylogenetic analysis suggests that S. agrestis is a sister species to Styrax faberi in Styracaceae.
| S-EPMC7954495 | biostudies-literature
Project description:Amomum tsao-ko (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. tsao-ko was determined using Illumina sequencing platform. The size of whole cp genome was 163,648 bp, containing a small single copy (SSC) region of 15,355 bp and a large single copy (LSC) region of 88,741 bp, which were separated by a pair of inverted repeat (IRs) regions (29,776 bp). The A. tsao-ko cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. tsao-ko cp genome is 36.02%. To investigate the evolution status of A. tsao-ko, as well as Zingiberales, a phylogenetic tree with A. tsao-ko and other 16 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. tsao-ko was closely related to Alpinia zerumbet.
| S-EPMC7748665 | biostudies-literature
Project description:Epidemics of infectious diseases threaten human health and society stability. Pharmacophagous plants are rich in bioactive compounds that constitute a safe drug library for antimicrobial agents. In this study, we have deciphered for the first time antibacterial ingredients and modes of the methanol-phase extract (MPE) from the fruit of Amomum villosum Lour. The results have revealed that the antibacterial rate of the MPE was 63.64%, targeting 22 species of common pathogenic bacteria. The MPE was further purified by high performance liquid chromatography (Prep-HPLC), and three different constituents (Fractions 1-3) were obtained. Of these, the Fraction 2 treatment significantly increased the cell membrane fluidity and permeability, reduced the cell surface hydrophobicity, and damaged the integrity of the cell structure, leading to the leakage of cellular macromolecules of Gram-positive and Gram-negative pathogens (p < 0.05). Eighty-nine compounds in Fraction 2 were identified by ultra HPLC-mass spectrometry (UHPLC-MS) analysis, among which 4-hydroxyphenylacetylglutamic acid accounted for the highest 30.89%, followed by lubiprostone (11.86%), miltirone (10.68%), and oleic acid (10.58%). Comparative transcriptomics analysis revealed significantly altered metabolic pathways in the representative pathogens treated by Fraction 2 (p < 0.05), indicating multiple antibacterial modes. Overall, this study first demonstrates the antibacterial activity of the MPE from the fruit of A. villosum Lour., and should be useful for its application in the medicinal and food preservative industries against common pathogens.
| S-EPMC10975419 | biostudies-literature