High Throughput Sequencing Advances and Future Challenges

Pervaiz, Tariq; Lotfi, Abolfazl; Haider, Muhammad Salman; Haifang, Jia; Fang, Jinggui

doi:10.4172/2329-9029.1000188

Cited by 7 publications

(5 citation statements)

References 90 publications

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“…A number of HTS platforms have been developed and are widely used, including the Illumina (e.g., HiSeq, MiSeq), Roche 454 GS FLX+, SOLiD 5500 series, and Ion Torrent/Ion Proton platforms. Currently, the majority of microbial ecology studies implement HTS by focusing on either targeted gene sequencing with phylogenetic or functional gene targets or on shotgun metagenome sequencing (Pervaiz et al, 2017 ).…”

Section: Methodological Approaches To Unravel the Composition And Funmentioning

confidence: 99%

Belowground Microbiota and the Health of Tree Crops

et al. 2018

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Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

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Section: Methodological Approaches To Unravel the Composition And Funmentioning

confidence: 99%

Belowground Microbiota and the Health of Tree Crops

et al. 2018

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“…In recent years, there have been remarkable advances in next-generation sequencing-based meta-omics, serving as a magnifying lens to unveil the structure and functions of the plant-associated microbial communities [ 19 ]. Currently available high-throughput sequencing approaches, such as the Illumina (e.g., HiSeq and MiSeq), Roche 454 GS FLX+, and Ion Torrent/Ion Proton platforms, have rapidly advanced and have been widely used in recent studies of plant-associated microbes [ 20 ]. In the past, studies on microbial communities mostly relied on the PCR amplification of a taxonomically relevant genomic marker, such as the hypervariable regions of the 16S rRNA gene to examine the bacterial diversity or the ITS region to examine the fungal diversity and taxonomic classification of the existing microbes.…”

Section: Meta-omics and Plant Phytobiome Studiesmentioning

confidence: 99%

Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm

Mannaa

Seo

2021

Plants

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Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes—differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions—are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant’s biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen–one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen–one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.

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“…At this moment, the high throughput sequencing (HTS) it is becoming more and more accessible and friendly, as this happens, more species are getting sequenced for multiple purposes including gene expression profiling, epigenomics, genomics, and transcriptomics approaches [25].…”

Section: Discussionmentioning

confidence: 99%

Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]

Salazar

Vergara

Jorquera

et al. 2019

Preprint

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Background Kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson] is a sub-tropical vine from the Actinidiaceae family native from China. This specie has an allohexaploid genome (from a diploid and autotetraploid parents) contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently there's no too much genomic and transcriptomic information about this species. In this low molecular knowledge context, the main goal of this work is to construct a tissue-specific de novo transcriptome assembly generating a differential expression analysis among these specific tissues to obtain new useful database for a better knowledge of vegetative, floral and fruit growth in different phenological states of Actinidia deliciosa cv. ‘Hayward’. Results In the present study we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at 4 development stages (7,50,120 and 160 days after flowering; DAF) in kiwifruit by using RNA-seq. We sequenced twenty-four libraries, obtaining 604,735,364 reads which were assembled using Trinity software. The first version of Actinidia deliciosa de novo transcriptome contained 142,025 contigs (x̅=1,044bp, N50=1,133bp). CEGMA and BUSCO were used for assembly quality assessment, obtaining close to 90.0% (35.1% partial) and over 85.0% (18.3% partial) of the ultra-conserved genes for eukaryote and plants, respectively. Annotation was performed with BLASTx against TAIR10 protein database and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs assembly without annotation. Conclusions These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of Actinidia deliciosa genes related to leaf, flower and fruit development. Thus, the present study provides a high valuable information, identifying over 20,000 exclusive genes including all tissue comparisons, which are associated with the proteins involved in different biological processes and molecular functions. Transcriptome assembly and refining as well as the assembly metric assessment, has implied an enough quality to be a putative database of this specie and high number of ultra-conserved proteins were found. With respect to transcriptome close to 65% of contigs did not match with any protein. Therefore, future functional annotation will be required in order to obtain a better knowledge of the tissue-specific development.

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High Throughput Sequencing Advances and Future Challenges

Cited by 7 publications

References 90 publications

Belowground Microbiota and the Health of Tree Crops

Belowground Microbiota and the Health of Tree Crops

Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm

Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]

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