scholarly journals Host adaptation through hybridization: Genome analysis of triticale powdery mildew reveals unique combination of lineage-specific effectors

2021 ◽  
Author(s):  
Marion Claudia Müller ◽  
Lukas Kunz ◽  
Johannes Peter Graf ◽  
Seraina Schudel ◽  
Beat Keller
Keyword(s):  
Powdery Mildew ◽  
Fungal Pathogens ◽  
Genetic Basis ◽  
Reference Genome ◽  
Resistance Breeding ◽  
Host Adaptation ◽  
Allelic Series ◽  
Hybrid Genome ◽  
Long Read ◽  
Bona Fide

The emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f.sp. tritici) and rye mildew (B.g. f.sp. secalis) pathogens have led to the emergence of a new mildew form (B.g. f.sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host-adaptation in triticale mildew has been hampered by the lack of a reference genome. Here we report the 141.4 Mb reference assembly of triticale mildew isolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All eleven triticale mildew chromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbour numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host-adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this we demonstrate the functional transfer of the SvrPm3 effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheat Pm3 allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of several Pm3 alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding.

scholarly journals Host adaptation through hybridization: Genome analysis of triticale powdery mildew reveals unique combination of lineage-specific effectors

2021 ◽  
Author(s):  
Marion C Müller ◽  
Lukas Kunz ◽  
Johannes Graf ◽  
Seraina Schudel ◽  
Beat Keller
Keyword(s):  
Powdery Mildew ◽  
Fungal Pathogens ◽  
Genetic Basis ◽  
Reference Genome ◽  
Resistance Breeding ◽  
Host Adaptation ◽  
Allelic Series ◽  
Hybrid Genome ◽  
Long Read ◽  
Bona Fide

The emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f.sp. tritici) and rye mildew (B.g. f.sp. secalis) pathogens have led to the emergence of a new mildew form (B.g. f.sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host-adaptation in triticale mildew has been hampered by the lack of a reference genome. Here we report the 141.4 Mb reference assembly of B.g. triticale isolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All eleven B.g. triticale chromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbour numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host-adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this we demonstrate the functional transfer of the SvrPm3 effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheat Pm3 allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of several Pm3 alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding.

scholarly journals A Reference Genome for the Nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris)

2021 ◽  
Author(s):  
Anna E Hiller ◽  
Robb T Brumfield ◽  
Brant C Faircloth
Keyword(s):  
Natural History ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Genetic Basis ◽  
Reference Genome ◽  
Nectar Robbing ◽  
Wild Female ◽  
Diverse Species ◽  
A Genome ◽  
Long Read

Abstract Black-throated Flowerpiercers (Diglossa brunneiventris) are one species representing a phenotypically specialized group of tanagers (Thraupidae) that have hooked bills which allow them to feed by stealing nectar from the base of flowers. Members of the genus are widely distributed in montane regions from Mexico to northern Argentina, and previous studies of Diglossa have focused on their systematics, phylogenetics, and interesting natural history. Despite numerous studies of species within the genus, no genome assembly exists to represent these nectivorous tanagers. We described the assembly of a genome sequence representing a museum-vouchered, wild, female Diglossa brunneiventris collected in Peru. By combining Pacific Biosciences Sequel long-read technology with 10X linked-read and reference-based scaffolding, we produced a 1.08 Gbp pseudochromosomal assembly including 600 scaffolds with a scaffold N50 of 67.3 Mbp, a scaffold L50 of 6, and a BUSCO completeness score of 95%. This new assembly improves representation of the diverse species that comprise the tanagers, improves on scaffold lengths and contiguity when compared to existing genomic resources for tanagers, and provides another avenue of research into the genetic basis of adaptations common to a nectivorous lifestyle among vertebrates.

scholarly journals A Hybrid Genome Assembly Resource for Podosphaera xanthii, the Main Causal Agent of Powdery Mildew Disease in Cucurbits

2020 ◽  
Author(s):  
Álvaro Polonio ◽  
Luis Díaz-Martínez ◽  
Dolores Fernández-Ortuño ◽  
Antonio de Vicente ◽  
Diego F. Romero ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Genome Assembly ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Causal Agent ◽  
Podosphaera Xanthii ◽  
Reference Genome Assembly ◽  
Long Reads ◽  
Hybrid Genome ◽  
Powdery Mildew Fungi

Podosphaera xanthii is the main causal agent of powdery mildew in cucurbits and, arguably, the most important fungal pathogen of cucurbit crops. Here, we present the first reference genome assembly for P. xanthii. We performed a hybrid genome assembly, using reads from Illumina NextSeq550 and PacBio Sequel S3. The short and long reads were assembled into 1,727 scaffolds with a N50 size of 163,173 bp, resulting in a 142 Mb genome size. The combination of homology-based and ab initio predictions allowed predicting 14,911 complete genes. Repetitive sequences comprised 76.2 % of the genome. Our P. xanthii genome assembly improves considerably the molecular resources for research on P. xanthii−cucurbit interactions and provides new opportunities for further genomics, transcriptomics and evolutionary studies in powdery mildew fungi.

NEW VARIETIES OF CURRANTS AND GOOSEBERRY BREEDING PLANTS

1970 ◽  
pp. 41-46
Author(s):  
O. D. Golyaeva ◽  
O. V. Kurashev ◽  
S. D. Knyazev ◽  
А. Yu. Bakhotskaya
Keyword(s):  
Powdery Mildew ◽  
Genetic Basis ◽  
Black Currant ◽  
Leaf Spots ◽  
Agricultural Sciences ◽  
Berry Crops ◽  
New Varieties ◽  
First Time ◽  
Red Currant

The main goal of the scientific institution was and remains to improve the assortment of fruit and berry crops for the development of domestic horticulture. Black currant breeding at VNIISPK was started by A.F Tamarova and continued by the doctor of agricultural Sciences T.P.Ogoltsova and doctor of agricultural Sciences S.D. Knyazev. A long-term breeding program has been developed. The main goals of the program are to create black currant cultivars with continuous resistance to diseases, first of all powdery mildew, as wells resistance to pests, i.e. bud mite. As a result of the long-term work, over 40 black currant cultivars have been developed, 14 of them are zoned. Red currant breeding was led by the candidate of agricultural Sciences L.V. Bayanova; since 2001 the work has been continued by the candidate of agricultural Sciences O.D. Golyaeva. ‘Heinemanns Rote Spӓtlese’, the descendant of R. multiflorum Kit., was involved in the red currant breeding for the first time in Russia. On its genetic basis, a series of late maturing cultivars with long and dense racemes was created. At the Institute, in total 21cultivars of red currants have been developed, 13 of them are zoned. At present, red currant cultivars make up 25.5% of the zoned assortment in Russia. The first research on gooseberries was stated by V.P. Semakin and A.F Tamarova; since 1992 the systematic gooseberry breeding has been carried out by the candidate of agricultural Sciences O.V. Kurashev. On the basis of Grossularia robusta, we have created gooseberry forms that are resistant to powdery mildew and leaf spots. These forms are highly productive, weakly thorned, having bush habit suitable for mechanized harvest. The result of breeding activities was the transfer of 6 gooseberry cultivars to State agricultural testing: ‘Solnechny Zaychik’, ‘Nekrasovsky’, ‘Yupiter’, ‘Zemlianichny’, ‘Moryachok’ and ‘Discovery’.

scholarly journals Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1

Genetics ◽  
2020 ◽  
Vol 217 (2) ◽  
Author(s):  
Antony V E Chapman ◽  
Matthew Hunt ◽  
Priyanka Surana ◽  
Valeria Velásquez-Zapata ◽  
Weihui Xu ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Fungal Pathogens ◽  
Novel Mutation ◽  
Exome Capture ◽  
Resistance Locus ◽  
Hordeum Vulgare L ◽  
Powdery Mildew Fungus ◽  
Pathogen Effectors ◽  
Cell Processes ◽  
Disease Resistances

Abstract Barley (Hordeum vulgare L.) Mla (Mildew resistance locus a) and its nucleotide-binding, leucine-rich-repeat receptor (NLR) orthologs protect many cereal crops from diseases caused by fungal pathogens. However, large segments of the Mla pathway and its mechanisms remain unknown. To further characterize the molecular interactions required for NLR-based immunity, we used fast-neutron mutagenesis to screen for plants compromised in MLA-mediated response to the powdery mildew fungus, Blumeria graminis f. sp. hordei. One variant, m11526, contained a novel mutation, designated rar3 (required for Mla6 resistance3), that abolishes race-specific resistance conditioned by the Mla6, Mla7, and Mla12 alleles, but does not compromise immunity mediated by Mla1, Mla9, Mla10, and Mla13. This is analogous to, but unique from, the differential requirement of Mla alleles for the co-chaperone Rar1 (required for Mla12 resistance1). We used bulked-segregant-exome capture and fine mapping to delineate the causal mutation to an in-frame Lys-Leu deletion within the SGS domain of SGT1 (Suppressor of G-two allele of Skp1, Sgt1ΔKL308–309), the structural region that interacts with MLA proteins. In nature, mutations to Sgt1 usually cause lethal phenotypes, but here we pinpoint a unique modification that delineates its requirement for some disease resistances, while unaffecting others as well as normal cell processes. Moreover, the data indicate that the requirement of SGT1 for resistance signaling by NLRs can be delimited to single sites on the protein. Further study could distinguish the regions by which pathogen effectors and host proteins interact with SGT1, facilitating precise editing of effector incompatible variants.

PSXII-2 Identification of candidate SNPs associated with high prolificacy in Romanov sheep

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 254-255
Author(s):  
Alexey V Shakhin ◽  
Arsen V Dotsev ◽  
Tatiana E Deniskova ◽  
Gottfried Brem ◽  
Natalia A Zinovieva
Keyword(s):  
Higher Education ◽  
Genetic Basis ◽  
Reference Genome ◽  
Unique Property ◽  
Candidate Snps ◽  
Merino Sheep ◽  
Sheep Breeds ◽  
Important Trait ◽  
Very High ◽  
Selection Of

Abstract Prolificacy is a very important trait in sheep. Romanov sheep, the well-known Russian sheep breed, are characterized by very high prolificacy; however, the genetic basis of this unique property of Romanov sheep is still unknown. It was reported that Ovine BMPR1B gene, located on the OAR6, is associated with prolificacy in several sheep breeds. The aim of our study was to identify candidate SNPs within BMPR1B gene, related to prolificacy. To achieve this goal, using NGS technology, we sequenced ovine BMPR1B gene in Romanov sheep (n = 6), which are characterized by high prolificacy (about 270 lambs per 100 ewes). The sequences of BMPR1B gene of Noire du Velay, Tan, Southdown and Australian Horned Merino sheep breeds as well as Asiatic mouflon (n = 1), which are characterized by significantly lower prolificacy (from 110 to 180 lambs per 100 ewes) were derived from publicly available sources and used for comparison. FST analysis performed in PLINK 1.9 program revealed 10 SNPs with values higher than 0.8. The majority of candidate SNPs under putative selection were localized in the region from 29,382,098 to 29,430,387 on OAR6 of Ovine reference genome (Oar_v3.1 (Ensembl release 98). Thus, we can suggest, that this region of the BMPR1B gene can be considered as the putative region, associated with high prolificacy of Romanov sheep. Additional studies will be needed to confirm the effect of identified candidate SNPs on prolificacy traits. The research results will be useful for artificial selection of sheep with higher prolific capacity, including the introduction of desired alleles in sheep populations using genome editing technologies. This work was supported by the Russian Ministry of Science and Higher Education No. 0445-2019-0024 and RFBR No. 20-516-56002.

scholarly journals Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions

2021 ◽  
pp. gr.275325.121
Author(s):  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Adam Sateriale ◽  
Karen L. Brooks ◽  
Alan Tracey ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Diarrheal Disease ◽  
Gene Copy ◽  
Future Research ◽  
Single Nucleotide Variants ◽  
Cryptosporidium Hominis ◽  
Entire Chromosome ◽  
Long Read ◽  
Subtelomeric Regions

Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum, Cryptosporidium hominis and Cryptosporidium tyzzeri. We made 1,926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis and C. tyzzeri revealed that most "missing" orthologs are found suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation and single nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

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