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1. Evolution of Phytophthora infestans on its potato host since the Irish potato famine

   https://doi.org/10.1038/s41467-024-50749-4  

   Coomber, Allison; Saville, Amanda; Ristaino, Jean Beagle (December 2024, Nature Communications)

   Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845–1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845–1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared tomodern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection. 

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2. Potato virus X : A global potato‐infecting virus and type member of the Potexvirus genus

   https://doi.org/10.1111/mpp.13163  

   Verchot, Jeanmarie (November 2021, Molecular Plant Pathology)

   Abstract TaxonomyPotato virus Xis the type‐member of the plant‐infectingPotexvirusgenus in the familyAlphaflexiviridae. Physical propertiesPotato virus X (PVX) virions are flexuous filaments 460–480 nm in length. Virions are 13 nm in diameter and have a helical pitch of 3.4 nm. The genome is approximately 6.4 kb with a 5′ cap and 3′ poly(A) terminus. PVX contains five open reading frames, four of which are essential for cell‐to‐cell and systemic movement. One protein encodes the viral replicase. Cellular inclusions, known as X‐bodies, occur near the nucleus of virus‐infected cells. HostsThe primary host is potato, but it infects a wide range of dicots. Diagnostic hosts includeDatura stramoniumandNicotiana tabacum. PVX is transmitted in nature by mechanical contact. Useful websitehttps://talk.ictvonline.org/ictv‐reports/ictv_online_report/positive‐sense‐rna‐viruses/w/alphaflexiviridae/1330/genus‐potexvirus 

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3. PL-4 (CIP596131.4): an Improved Potato Haploid Inducer

   https://doi.org/10.1007/s12230-021-09839-y  

   Ordoñez, Benny; Santayana, Monica; Aponte, Mariela; Henry, Isabelle M.; Comai, Luca; Eyzaguirre, Raúl; Lindqvist-Kreuze, Hannele; Bonierbale, Merideth (July 2021, American Journal of Potato Research)

   Abstract Dihaploid production from elite tetraploid cultivars is key to both traditional and novel breeding approaches that seek to simplify potato genetics. For this purpose, efficient and widely compatible haploid inducers (HIs) are needed. We compared PL-4, a new HI developed at the International Potato Center, to known HIs IvP101 and IvP35. By pollination of elite tetraploid breeding lines, we showed that PL-4 performed significantly better and had a homogeneous response regardless of the genetic background of the pistillate parents, on the most important efficiency traits—number of dihaploids per 100 fruits and haploid induction rate. Moreover, PL-4 exhibited a reduced proportion of hybrid seeds, a convenient trait for efficient screening. In this context, we recommend PL-4 as an enhanced HI for the potato breeding community. 

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4. SpudDB: a database for accessing potato genomic data

   https://doi.org/10.1093/genetics/iyae205  

   Hamilton, John P; Brose, Julia; Buell, C Robin (December 2024, GENETICS)

   Harris, T (Ed.)

   Abstract Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1–3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit the identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists, and breeders to continue to improve this key food crop. 

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5. Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

   https://doi.org/10.1101/845818  

   Petek, Marko; Zagorščak, Maja; Ramšak, Živa; Sanders, Sheri; Tomaž, Špela; Tseng, Elizabeth; Zouine, Mohamed; Coll, Anna; Gruden, Kristina (July 2020, Scientific data)

   Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes. 

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