International Journal of Molecular Sciences

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17 pages, 7733 KiB

Open AccessArticle

Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations

by Delphine Vincent and Rudi Appels

Int. J. Mol. Sci. 2024, 25(16), 8614; https://doi.org/10.3390/ijms25168614 - 7 Aug 2024

Viewed by 323

Abstract

Triticum aestivum is an important crop whose reference genome (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.1) offers a valuable resource for understanding wheat genetic structure, improving agronomic traits, and developing new cultivars. A key aspect of gene model annotation is protein-level evidence [...] Read more.

Triticum aestivum is an important crop whose reference genome (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.1) offers a valuable resource for understanding wheat genetic structure, improving agronomic traits, and developing new cultivars. A key aspect of gene model annotation is protein-level evidence of gene expression obtained from proteomics studies, followed up by proteogenomics to physically map proteins to the genome. In this research, we have retrieved the largest recent wheat proteomics datasets publicly available and applied the Basic Local Alignment Search Tool (tBLASTn) algorithm to map the 861,759 identified unique peptides against IWGSC RefSeq v2.1. Of the 92,719 hits, 83,015 unique peptides aligned along 33,612 High Confidence (HC) genes, thus validating 31.4% of all wheat HC gene models. Furthermore, 6685 unique peptides were mapped against 3702 Low Confidence (LC) gene models, and we argue that these gene models should be considered for HC status. The remaining 2934 orphan peptides can be used for novel gene discovery, as exemplified here on chromosome 4D. We demonstrated that tBLASTn could not map peptides exhibiting mid-sequence frame shift. We supply all our proteogenomics results, Galaxy workflow and Python code, as well as Browser Extensible Data (BED) files as a resource for the wheat community via the Apollo Jbrowse, and GitHub repositories. Our workflow could be applied to other proteomics datasets to expand this resource with proteins and peptides from biotically and abiotically stressed samples. This would help tease out wheat gene expression under various environmental conditions, both spatially and temporally. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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14 pages, 3357 KiB

Open AccessArticle

Mining the Australian Grains Gene Bank for Rust Resistance in Barley

by Md Arifuzzaman, Matthias Jost, Meinan Wang, Xianming Chen, Dragan Perovic, Robert F. Park, Matthew Rouse, Kerrie Forrest, Matthew Hayden, Ghazanfar Abbas Khan and Peter M. Dracatos

Int. J. Mol. Sci. 2023, 24(13), 10860; https://doi.org/10.3390/ijms241310860 - 29 Jun 2023

Cited by 1 | Viewed by 1595

Abstract

Global barley production is threatened by plant pathogens, especially the rusts. In this study we used a targeted genotype-by-sequencing (GBS) assisted GWAS approach to identify rust resistance alleles in a collection of 287 genetically distinct diverse barley landraces and historical cultivars available in [...] Read more.

Global barley production is threatened by plant pathogens, especially the rusts. In this study we used a targeted genotype-by-sequencing (GBS) assisted GWAS approach to identify rust resistance alleles in a collection of 287 genetically distinct diverse barley landraces and historical cultivars available in the Australian Grains Genebank (AGG) and originally sourced from Eastern Europe. The accessions were challenged with seven US-derived cereal rust pathogen races including Puccinia hordei (Ph-leaf rust) race 17VA12C, P. coronata var. hordei (Pch-crown rust) race 91NE9305 and five pathogenically diverse races of P. striiformis f. sp. hordei (Psh-stripe rust) (PSH-33, PSH-48, PSH-54, PSH-72 and PSH-100) and phenotyped quantitatively at the seedling stage. Novel resistance factors were identified on chromosomes 1H, 2H, 4H and 5H in response to Pch, whereas a race-specific QTL on 7HS was identified that was effective only to Psh isolates PSH-72 and PSH-100. A major effect QTL on chromosome 5HL conferred resistance to all Psh races including PSH-72, which is virulent on all 12 stripe rust differential tester lines. The same major effect QTL was also identified in response to leaf rust (17VA12C) suggesting this locus contains several pathogen specific rust resistance genes or the same gene is responsible for both leaf rust and stripe rust resistance. Twelve accessions were highly resistant to both leaf and stripe rust diseases and also carried the 5HL QTL. We subsequently surveyed the physical region at the 5HL locus for across the barley pan genome variation in the presence of known resistance gene candidates and identified a rich source of high confidence protein kinase and antifungal genes in the QTL region. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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13 pages, 3466 KiB

Open AccessArticle

The Effect of Scale Insects on Growth Parameters of cv. Chardonnay and cv. Sauvignon Blanc Grapevines Grown in a Greenhouse

by Paul D. Cooper, Thy T. Truong, Andras Keszei, Teresa Neeman and Kenneth W. Webster

Int. J. Mol. Sci. 2023, 24(2), 1544; https://doi.org/10.3390/ijms24021544 - 12 Jan 2023

Viewed by 1419

Abstract

Plants can respond to insects that feed with stylet mouthparts using various processes that are initiated via the salicylic acid metabolic pathway. In Australia, scale insects of the genus Parthenolecanium can cause economic damage to grapevines as they feed on the vines and [...] Read more.

Plants can respond to insects that feed with stylet mouthparts using various processes that are initiated via the salicylic acid metabolic pathway. In Australia, scale insects of the genus Parthenolecanium can cause economic damage to grapevines as they feed on the vines and produce honeydew as a waste by-product, which supports the growth of black sooty mould on fruit and leaves, potentially affecting the plant growth and yield. Using rootlings of Sauvignon Blanc (SB, resistant) and Chardonnay (Char, susceptible), the growth and production of volatile organic compounds (VOCs) following exposure to scale insect infestations were measured under controlled greenhouse conditions. At harvest, the numbers of scale insects per five leaves were higher on plants infested at the start of the study compared with the control plants. Infested SB had increased dry root and shoot mass compared with the SB control, which was also the case with Char (control and infested). Leaf volatiles differed between cultivars in response to scale infestation. Benzyl alcohol decreased among infested SB plants compared with the other treatments. A change in the salicylic acid pathway as indicated by the change in benzyl alcohol may cause the increased growth in SB associated with the increased scale insect infestation. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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20 pages, 2459 KiB

Open AccessArticle

Unique and Shared Proteome Responses of Rice Plants (Oryza sativa) to Individual Abiotic Stresses

by Fatemeh Habibpourmehraban, Brian J. Atwell and Paul A. Haynes

Int. J. Mol. Sci. 2022, 23(24), 15552; https://doi.org/10.3390/ijms232415552 - 8 Dec 2022

Cited by 7 | Viewed by 1453

Abstract

Food safety of staple crops such as rice is of global concern and is at the top of the policy agenda worldwide. Abiotic stresses are one of the main limitations to optimizing yields for sustainability, food security and food safety. We analyzed proteome [...] Read more.

Food safety of staple crops such as rice is of global concern and is at the top of the policy agenda worldwide. Abiotic stresses are one of the main limitations to optimizing yields for sustainability, food security and food safety. We analyzed proteome changes in Oryza sativa cv. Nipponbare in response to five adverse abiotic treatments, including three levels of drought (mild, moderate, and severe), soil salinization, and non-optimal temperatures. All treatments had modest, negative effects on plant growth, enabling us to identify proteins that were common to all stresses, or unique to one. More than 75% of the total of differentially abundant proteins in response to abiotic stresses were specific to individual stresses, while fewer than 5% of stress-induced proteins were shared across all abiotic constraints. Stress-specific and non-specific stress-responsive proteins identified were categorized in terms of core biological processes, molecular functions, and cellular localization. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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19 pages, 1753 KiB

Open AccessArticle

Metabolic Pathways for Observed Impacts of Crop Load on Floral Induction in Apple

by Priyanka Reddy, Tim Plozza, Vilnis Ezernieks, Dario Stefanelli, Alessio Scalisi, Ian Goodwin and Simone Rochfort

Int. J. Mol. Sci. 2022, 23(11), 6019; https://doi.org/10.3390/ijms23116019 - 27 May 2022

Cited by 8 | Viewed by 2149

Abstract

The triggers of biennial bearing are thought to coincide with embryonic development in apple and occurs within the first 70 days after full bloom (DAFB). Strong evidence suggests hormonal signals are perceived by vegetative apple spur buds to induce flowering. The hormonal response [...] Read more.

The triggers of biennial bearing are thought to coincide with embryonic development in apple and occurs within the first 70 days after full bloom (DAFB). Strong evidence suggests hormonal signals are perceived by vegetative apple spur buds to induce flowering. The hormonal response is typically referred to as the floral induction (FI) phase in bud meristem development. To determine the metabolic pathways activated in FI, young trees of the biennial bearing cultivar ‘Nicoter’ and the less susceptible cultivar ‘Rosy Glow’ were forced into an alternate cropping cycle over five years and an inverse relationship of crop load and return bloom was established. Buds were collected over a four-week duration within 70 DAFB from trees that had maintained a four-year biennial bearing cycle. Metabolomics profiling was undertaken to determine the differentially expressed pathways and key signalling molecules associated with biennial bearing. Marked metabolic differences were observed in trees with high and low crop load treatments. Significant effects were detected in members of the phenylpropanoid pathway comprising hydroxycinnamates, salicylates, salicylic acid biosynthetic pathway intermediates and flavanols. This study identifies plant hormones associated with FI in apples using functional metabolomics analysis. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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Review

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15 pages, 2741 KiB

Open AccessReview

A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics

by Thomas Farrall, Jeremy Brawner, Adrian Dinsdale and Monica Kehoe

Int. J. Mol. Sci. 2024, 25(15), 8348; https://doi.org/10.3390/ijms25158348 - 30 Jul 2024

Viewed by 424

Abstract

Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to [...] Read more.

Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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34 pages, 2919 KiB

Open AccessReview

RNA-Based Control of Fungal Pathogens in Plants

by Christopher W. G. Mann, Anne Sawyer, Donald M. Gardiner, Neena Mitter, Bernard J. Carroll and Andrew L. Eamens

Int. J. Mol. Sci. 2023, 24(15), 12391; https://doi.org/10.3390/ijms241512391 - 3 Aug 2023

Cited by 7 | Viewed by 4132

Abstract

Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20–40% [...] Read more.

Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20–40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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16 pages, 1753 KiB

Open AccessReview

Phloem Sap Composition: What Have We Learnt from Metabolomics?

by Louis Broussard, Cyril Abadie, Julie Lalande, Anis M. Limami, Jérémy Lothier and Guillaume Tcherkez

Int. J. Mol. Sci. 2023, 24(8), 6917; https://doi.org/10.3390/ijms24086917 - 7 Apr 2023

Cited by 9 | Viewed by 4234

Abstract

Phloem sap transport is essential for plant nutrition and development since it mediates redistribution of nutrients, metabolites and signaling molecules. However, its biochemical composition is not so well-known because phloem sap sampling is difficult and does not always allow extensive chemical analysis. In [...] Read more.

Phloem sap transport is essential for plant nutrition and development since it mediates redistribution of nutrients, metabolites and signaling molecules. However, its biochemical composition is not so well-known because phloem sap sampling is difficult and does not always allow extensive chemical analysis. In the past years, efforts have been devoted to metabolomics analyses of phloem sap using either liquid chromatography or gas chromatography coupled with mass spectrometry. Phloem sap metabolomics is of importance to understand how metabolites can be exchanged between plant organs and how metabolite allocation may impact plant growth and development. Here, we provide an overview of our current knowledge of phloem sap metabolome and physiological information obtained therefrom. Although metabolomics analyses of phloem sap are still not numerous, they show that metabolites present in sap are not just sugars and amino acids but that many more metabolic pathways are represented. They further suggest that metabolite exchange between source and sink organs is a general phenomenon, offering opportunities for metabolic cycles at the whole-plant scale. Such cycles reflect metabolic interdependence of plant organs and shoot–root coordination of plant growth and development. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Australia)

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