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1. Spray‐induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control

   https://doi.org/10.1111/mpp.13361  

   McRae, Amanda_G; Taneja, Jyoti; Yee, Kathleen; Shi, Xinyi; Haridas, Sajeet; LaButti, Kurt; Singan, Vasanth; Grigoriev, Igor_V; Wildermuth, Mary_C (June 2023, Molecular Plant Pathology)

   Abstract Spray‐induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double‐stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole‐fungicide targetcytochrome P45051 (CYP51) in theGolovinomyces orontii–Arabidopsis thalianapathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation:apoptosis‐antagonizing transcription factorin essential cellular metabolism and stress response; lipid catabolism geneslipase a,lipase 1, andacetyl‐CoA oxidasein energy production;and genes involved in manipulation of the plant host via abscisic acid metabolism (9‐cis‐epoxycarotenoid dioxygenase,xanthoxin dehydrogenase, and a putativeabscisic acid G‐protein coupled receptor) and secretion of the effector protein,effector candidate 2. Powdery mildew is the dominant disease impacting grapes and extensive powdery mildew resistance to applied fungicides has been reported. We therefore developed SIGS for theErysiphe necator–Vitis viniferasystem and tested six successful targets identified using theG. orontii–A. thalianasystem. For all targets tested, a similar reduction in powdery mildew disease was observed between systems. This indicates screening of broadly conserved targets in theG. orontii–A. thalianapathosystem identifies targets and processes for the successful control of other powdery mildew fungi. The efficacy of SIGS on powdery mildew fungi makes SIGS an exciting prospect for commercial powdery mildew control. 

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2. Physical Mapping of Pm57, a Powdery Mildew Resistance Gene Derived from Aegilops searsii

   https://doi.org/10.3390/ijms21010322  

   Dong, Zhenjie; Tian, Xiubin; Ma, Chao; Xia, Qing; Wang, Beilin; Chen, Qifan; Sehgal, Sunish K.; Friebe, Bernd; Li, Huanhuan; Liu, Wenxuan (January 2020, International Journal of Molecular Sciences)

   Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is one of many severe diseases that threaten bread wheat (Triticum aestivum L.) yield and quality worldwide. The discovery and deployment of powdery mildew resistance genes (Pm) can prevent this disease epidemic in wheat. In a previous study, we transferred the powdery mildew resistance gene Pm57 from Aegilops searsii into common wheat and cytogenetically mapped the gene in a chromosome region with the fraction length (FL) 0.75–0.87, which represents 12% segment of the long arm of chromosome 2Ss#1. In this study, we performed RNA-seq using RNA extracted from leaf samples of three infected and mock-infected wheat-Ae. searsii 2Ss#1 introgression lines at 0, 12, 24, and 48 h after inoculation with Bgt isolates. Then we designed 79 molecular markers based on transcriptome sequences and physically mapped them to Ae. searsii chromosome 2Ss#1- in seven intervals. We used these markers to identify 46 wheat-Ae. searsii 2Ss#1 recombinants induced by ph1b, a deletion mutant of pairing homologous (Ph) genes. After analyzing the 46 ph1b-induced 2Ss#1L recombinants in the region where Pm57 is located with different Bgt-responses, we physically mapped Pm57 gene on the long arm of 2Ss#1 in a 5.13 Mb genomic region, which was flanked by markers X67593 (773.72 Mb) and X62492 (778.85 Mb). By comparative synteny analysis of the corresponding region on chromosome 2B in Chinese Spring (T. aestivum L.) with other model species, we identified ten genes that are putative plant defense-related (R) genes which includes six coiled-coil nucleotide-binding site-leucine-rich repeat (CNL), three nucleotide-binding site-leucine-rich repeat (NL) and a leucine-rich receptor-like repeat (RLP) encoding proteins. This study will lay a foundation for cloning of Pm57, and benefit the understanding of interactions between resistance genes of wheat and powdery mildew pathogens. 

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3. Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

   https://doi.org/10.1093/g3journal/jkab033  

   Cochetel, Noé; Minio, Andrea; Massonnet, Mélanie; Vondras, Amanda M; Figueroa-Balderas, Rosa; Cantu, Dario (April 2021, G3 Genes|Genomes|Genetics)

   Morrell, P (Ed.)

   Abstract Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser, annotation, and Blast tool for Trayshed are available at www.grapegenomics.com. 

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4. A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki

   https://doi.org/10.1093/g3journal/jkad234  

   Eastman, Katharine E; Pendleton, Amanda L; Shaikh, Mearaj A; Suttiyut, Thiti; Ogas, Raeya; Tomko, Paxton; Gavelis, Gregory; Widhalm, Joshua R; Wisecaver, Jennifer H (October 2023, G3: Genes, Genomes, Genetics)

   Mallarino, R (Ed.)

   Abstract Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These “photosynthetic animals” incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals. 

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5. Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids

   https://doi.org/10.1093/gigascience/giad064  

   Lötter, Anneri; Duong, Tuan A; Candotti, Julia; Mizrachi, Eshchar; Wegrzyn, Jill L; Myburg, Alexander A (December 2022, GigaScience)

   Abstract BackgroundDe novo phased (haplo)genome assembly using long-read DNA sequencing data has improved the detection and characterization of structural variants (SVs) in plant and animal genomes. Able to span across haplotypes, long reads allow phased, haplogenome assembly in highly outbred organisms such as forest trees. Eucalyptus tree species and interspecific hybrids are the most widely planted hardwood trees with F1 hybrids of Eucalyptus grandis and E. urophylla forming the bulk of fast-growing pulpwood plantations in subtropical regions. The extent of structural variation and its effect on interspecific hybridization is unknown in these trees. As a first step towards elucidating the extent of structural variation between the genomes of E. grandis and E. urophylla, we sequenced and assembled the haplogenomes contained in an F1 hybrid of the two species. FindingsUsing Nanopore sequencing and a trio-binning approach, we assembled the separate haplogenomes (566.7 Mb and 544.5 Mb) to 98.0% BUSCO completion. High-density SNP genetic linkage maps of both parents allowed scaffolding of 88.0% of the haplogenome contigs into 11 pseudo-chromosomes (scaffold N50 of 43.8 Mb and 42.5 Mb for the E. grandis and E. urophylla haplogenomes, respectively). We identify 48,729 SVs between the two haplogenomes providing the first detailed insight into genome structural rearrangement in these species. The two haplogenomes have similar gene content, 35,572 and 33,915 functionally annotated genes, of which 34.7% are contained in genome rearrangements. ConclusionsKnowledge of SV and haplotype diversity in the two species will form the basis for understanding the genetic basis of hybrid superiority in these trees. 

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