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Insights into plastome of Fagonia indica Burm.f. (Zygophyllaceae): organization, annotation and phylogeny.

ABSTRACT: The enhanced understanding of chloroplast genomics would facilitate various biotechnology applications; however, the chloroplast (cp) genome / plastome characteristics of plants like Fagonia indica Burm.f. (family Zygophyllaceae), which have the capability to grow in extremely hot sand desert, have been rarely understood. The de novo genome sequence of F. indica using the Illumina high-throughput sequencing technology determined 128,379 bp long cp genome, encode 115 unique coding genes. The present study added the evidence of the loss of a copy of the IR in the cp genome of the taxa capable to grow in the hot sand desert. The maximum likelihood analysis revealed two distinct sub-clades i.e. Krameriaceae and Zygophyllaceae of the order Zygophyllales, nested within fabids.

SUBMITTER: Elshikh MS

PROVIDER: S-EPMC8913386 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Insights into plastome of Fagonia indica Burm.f. (Zygophyllaceae): organization, annotation and phylogeny.

Elshikh Mohamed S MS Ajmal Ali Mohammad M Al-Hemaid Fahad F Yong Kim Soo S Elangbam Meena M Bahadur Gurung Arun A Mukherjee Prasanjit P El-Zaidy Mohamed M Lee Joongku J

Saudi journal of biological sciences 20211112 3

The enhanced understanding of chloroplast genomics would facilitate various biotechnology applications; however, the chloroplast (cp) genome / plastome characteristics of plants like Fagonia indica Burm.f. (family Zygophyllaceae), which have the capability to grow in extremely hot sand desert, have been rarely understood. The de novo genome sequence of F. indica using the Illumina high-throughput sequencing technology determined 128,379 bp long cp genome, encode 115 unique c ...[more]

PMID: 35280582

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Project description:Fagonia indica Burm.f. is known for its anti-infective character and has been studied in the present work as a synergistic remedy against resistant bacterial strains. Initially, phytochemicals were quantified in n-Hexane (n-Hex), ethyl acetate (E.A), methanol (MeOH), and aqueous (Aq.) extracts by Total Phenolic Content (TPC), Total Flavonoid Content (TFC) and Reverse Phase High Performance Liquid Chromatography (RP-HPLC) analysis. Later, after establishing an antibacterial resistance profile for extracts and antibiotics against gram-positive and gram-negative strains, synergism was evaluated in combination with cefixime through time-kill kinetics and bacterial protein estimation studies. Topographic images depicting synergism were obtained by scanning electron microscopy for Methicilin-resistant Staphylococcus aureus (MRSA) and Resistant Escherichia coli (R.E. coli). Results showed the presence of maximum phenolic (28.4 ± 0.67 μg GAE/mg extract) and flavonoid (11 ± 0.42 μg QE/mg extract) contents in MeOH extract. RP-HPLC results also displayed maximum polyphenols in MeOH extract followed by E.A extract. Clinical strains were resistant to cefixime whereas these were moderately inhibited by all extracts (MIC 150-300 µg/ml) except Aq. extract. E.A and n-Hex extracts demonstrated maximum synergism (Fractional inhibitory concentration index (FICI) 0.31) against R.E. coli. The n-Hex extract displayed total synergism against R.P. a with a 4-fold reduction in cefixime dose. Time-kill kinetics showed maximum inhibition of gram-negative bacterial growth from 3 to 12 h when treated at FICI and 2FICI values with > 10-fold reduction of the extracts' dose. All combinations demonstrate > 70 % protein content inhibition with bacterial cell wall disruption in SEM images. Fortunately, FICI concentrations have low hemolytic potential (<5%). Conclusively, F. indica extracts can mitigate antimicrobial resistance against cefixime and can be investigated in detail by in vivo and mechanistic studies.

Project description:Background and aimsRhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya-Hengduan Mountains where the genus is most diverse.MethodsWe reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to the Himalaya-Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of Rhododendron, especially the two species-rich subgenera Rhododendron and Hymenanthes that comprise >90 % of Rhododendron species in the Himalaya-Hengduan Mountains.Key resultsThe full plastid dataset produced a well-resolved and supported phylogeny of Rhododendron. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies suggested strongly that reticulation events may have occurred in the deep lineage history of the genus. Within Rhododendron, subgenus Therorhodion diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core Rhododendron. Diversification in subgenus Rhododendron accelerated c. 16.6 Mya and then became fairly continuous. Conversely, Hymenanthes diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya-Hengduan Mountains, subgenus Rhododendron contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in Hymenanthes contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification.ConclusionsThe 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for Rhododendron, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of Rhododendron.

Project description:Background and aimsThe genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study.MethodsIn this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families.ResultsOur phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species.ConclusionsOur results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.

Dataset Information

Insights into plastome of Fagonia indica Burm.f. (Zygophyllaceae): organization, annotation and phylogeny.

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Insights into plastome of <i>Fagonia indica</i> Burm.f. (Zygophyllaceae)<i>:</i> organization, annotation and phylogeny.

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