Next Generation Sequencing - Advances, Applications and Challenges

Kulski, Jerzy K.

doi:10.5772/60489

Cited by 50 publications

(3 citation statements)

References 77 publications

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“…In mammals, the figure may be 1/ 400 bp. Interestingly, earlier comparisons of MHC ancestral haplotypes revealed sequence diversity sufficient to prevent recombination according to Radman's predictions (Gaudieri et al, 1997(Gaudieri et al, , 1999Longman-Jacobsen et al, 2003;Lloyd et al, 2016). The careful study by Smith et al (2006) was also consistent with the Radman number for mammals.…”

Section: Mechanismssupporting

confidence: 55%

Commentary: Conserved polymorphic sequences protect themselves for future challenges

Dawkins

Lloyd

2022

Front. Genet.

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Section: Mechanismssupporting

confidence: 55%

Commentary: Conserved polymorphic sequences protect themselves for future challenges

Dawkins

Lloyd

2022

Front. Genet.

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“…Final barcoded libraries were quantified using the Ion Library TaqMan Quantitation Kit and an equimolar pool of 12 samples was prepared at a final concentration of 50 pM. Template preparation and chip loading were performed on the Ion Chef System (Thermo Fisher Scientific), whereas sequencing was carried out on the Ion PGM Sequencer using an Ion 318™ Chip v2 (Thermo Fisher Scientific), which can deliver up to 5 million reads per run, with an average length of 200-300 base pairs (Kulski, 2016). Data analysis.…”

Section: Ion Pgm Sequencingmentioning

confidence: 99%

“…Although these methods have permitted the finding of several trypanosomatid (Bartolomé et al, 2018;Tripodi et al, 2018) and nosematid species (Li et al, 2012) in Bombus specimens, their technical limitations urge the use of more powerful tools to better assess the extent of parasite diversity. Nowadays, the most comprehensive and cost-effective way to investigate this matter at a large scale is to apply high-throughput sequencing methods, which have much greater depth and resolution than Sanger sequencing (Kulski, 2016) and enable the simultaneous identification of multiple pathogens across large numbers of samples without having to clone the amplicons.…”

Section: Introductionmentioning

confidence: 99%

Wide diversity of parasites in Bombus terrestris (Linnaeus, 1758) revealed by a high‐throughput sequencing approach

Bartolomé

Jabal-Uriel

Buendía-Abad

et al. 2020

Environmental Microbiology

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Summary Assessing the extent of parasite diversity requires the application of appropriate molecular tools, especially given the growing evidence of multiple parasite co‐occurrence. Here, we compared the performance of a next‐generation sequencing technology (Ion PGM ™ System) in 12 Bombus terrestris specimens that were PCR‐identified as positive for trypanosomatids (Leishmaniinae) in a previous study. These bumblebees were also screened for the occurrence of Nosematidae and Neogregarinorida parasites using both classical protocols (either specific PCR amplification or amplification with broad‐range primers plus Sanger sequencing) and Ion PGM sequencing. The latter revealed higher parasite diversity within individuals, especially among Leishmaniinae (which were present as a combination of Lotmaria passim, Crithidia mellificae and Crithidia bombi), and the occurrence of taxa never reported in these hosts: Crithidia acanthocephali and a novel neogregarinorida species. Furthermore, the complementary results produced by the different sets of primers highlighted the convenience of using multiple markers to minimize the chance of some target organisms going unnoticed. Altogether, the deep sequencing methodology offered a more comprehensive way to investigate parasite diversity than the usual identification methods and provided new insights whose importance for bumblebee health should be further analysed.

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16S rRNA gene‐based identification and plant growth‐promoting potential of cultivable endophytic bacteria

Raimi

Adeleke

2023

Agronomy Journal

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Endophytic bacteria play essential roles in plant growth and fitness through nitrogen fixation, nutrient solubilization, and phytohormone production. However, the plant growth-promoting (PGP) potential of endophytic microorganisms inhabiting vegetables is underexplored. Thus, this study investigated the endophytic bacteria of vegetable crops for their PGP properties using the culture-dependent technique. Recovered isolates were identified by sequencing the partial 16S rRNA gene using Sanger sequencing. The isolated endophytic bacteria belonged to 15 genera and 39 different species. Bacillus, Enterobacter, Pantoea, and Pseudomonas were the predominant genera and had high phosphate solubilization and siderophore production potential. The isolates differentially produced indole-3-acetic acid and ammonium in the range 0.14-44.48 μg mL -1 and 0.77-93.24 mg L -1 , respectively. Pseudomonas azotoformans, Stenotrophomonas maltophilia, and Serratia liquefaciens showed a high level of siderophore production, which was not significantly (p > 0.05) different across the plant and organ types. More than 21% of endophytes could produce gelatinase, protease, amylase, and cellulase, contributing to their diverse ecosystem functions. Bacterial density and species composition varied across the vegetable species, organs, and farm locations but were higher in the stems compared with other organs. However, the vegetable organ had no significant (p > 0.05) influence on the bacterial population density, except for the interaction of plant species and organs.Overall, this study provides basic knowledge about the cultivable endophytic bacterial community of vegetables and reveals diverse endophytic bacteria useful in bioinoculant formulations for improving crop productivity.

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Next Generation Sequencing - Advances, Applications and Challenges

Cited by 50 publications

References 77 publications

Commentary: Conserved polymorphic sequences protect themselves for future challenges

Commentary: Conserved polymorphic sequences protect themselves for future challenges

Wide diversity of parasites in Bombus terrestris (Linnaeus, 1758) revealed by a high‐throughput sequencing approach

16S rRNA gene‐based identification and plant growth‐promoting potential of cultivable endophytic bacteria

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