Molecular Evolution

Clark, David P.; Pazdernik, Nanette J.; McGehee, Michelle R.

doi:10.1016/b978-0-12-813288-3.00029-x

Cited by 6 publications

(8 citation statements)

References 14 publications

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“…N. koreensis is an ammonia-oxidizing soil archaea belonging to the phylum Thaumarchaeota , which is an anaerobic bacterium and ubiquitous microbes in marine, freshwater, and terrestrial environments [ 52 ]. However, anaerobic bacteria generate energy by the oxidation of Fe 2+ compounds to Fe 3+ [ 53 ]. As an anaerobic bacterium, Ca.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

Jia

Xiao

et al. 2022

BMC Microbiol

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Background Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant. Results The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. Conclusions It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.

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Section: Discussionmentioning

confidence: 99%

Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

Jia

Xiao

et al. 2022

BMC Microbiol

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“…According to the molecular evolution principle, the rate of evolution of functionally important portions of the genome is slower than the rest of the cellular molecular regions. Hence, gene sequences that are useful for survival and other crucial functions are conserved [ 96 ], especially in closely related species. Homology-based annotations exploit this fact, to predict and annotate genes by identifying significant matches from a well annotated genome sequence by employing alignment tools such as BLAST.…”

Section: Comparative Annotation Methodsmentioning

confidence: 99%

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Ejigu

Jung

2020

Biology

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Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.

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“…A thermostable DNA polymerase enzyme copies the target DNA in PCR in the presence of nucleotides and specific primers. The target DNA is exponentially amplified by repeated heating and cooling cycles in a thermocycler that results in rounds of target DNA denaturation, primer hybridisation and primer extension (Clark et al., 2019). PCR is an exemplar detection assay and is required for the initial diagnosis of a disease.…”

Section: Molecular Tools For the Detection Of Silkworm Pathogensmentioning

confidence: 99%

Molecular diagnostics in sericulture: A paradigm shift towards disease diagnosis in silkworms

Deepika,

Ramesh,

Kumar

et al. 2024

Entomologia Exp Applicata

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Sericulture, the practice of rearing silkworms for the production of silk, is an essential agro‐based industry in several countries. However, silkworms are susceptible to a variety of diseases caused by viruses, bacteria and parasites, which may have a significant negative impact on global silk production. Traditional methods of pathogen identification, such as microscopy and laboratory culturing, have limitations in terms of accuracy and efficiency. The development of molecular techniques for pathogen identification has revolutionised the field of sericulture over the last decade. Genomic DNA and RNA‐based molecular techniques allow for the rapid and accurate detection of disease‐causing pathogens in silkworms. Molecular diagnosis has several advantages over traditional methods, including increased sensitivity and specificity, shorter turnaround time and the ability to detect pathogens that are difficult to culture or visualise under a microscope. Molecular techniques have been applied to detect several important pathogens of silkworms, including Nosema sp., nucleopolyhedrovirus, cypovirus, iflavirus and bidensovirus. The use of molecular diagnostics in sericulture is immensely important as the demand for high‐quality silk increases globally and the assessment of emerging pathogens associated with crop loss is essential. Major advancements in the improvement and application of molecular methods for diagnosing widespread silkworm pathogens are discussed.

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Molecular Evolution

Cited by 6 publications

References 14 publications

Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Molecular diagnostics in sericulture: A paradigm shift towards disease diagnosis in silkworms

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