Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.

To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with a very low haplotype switch-error rate (<0.025). The haplophase alignment identified > 25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as a reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated with abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unveil the molecular bases of clonal phenotypic variation.

Prognostic indicators in dogs with intra-hepatic portal hypertension.

Objectives: The primary goals of this retrospective study were to describe a population of dogs with portal hypertension secondary to liver disease, and to assess whether prognosis could be inferred from historical, clinical, and clinicopathological data. Animals and procedures: Dogs (N = 76) diagnosed with intrahepatic portal hypertension between 2011 and 2020 were included; dogs with known congenital hepatic anomalies were excluded. Effect on survival was assessed using univariable and multivariable Cox proportional hazards models for historical, clinical, and clinicopathological variables. Results: Dogs survived for a median of 14 d (range: 0 to 2028 d), with 31.6% being euthanized within 2 d of diagnosis and 23.7% surviving longer than 2 mo. Presence of jaundice and duration of clinical signs, expressed in days, were significantly associated with outcome in the univariable analysis (HR = 1.846, 95% CI: 1.094 to 3.117, P = 0.02; HR = 0.995, 95% CI: 0.990 to 1.000, P = 0.033, respectively). However, only presence of jaundice was significantly associated with increased hazard of death in the multivariable analysis. Conclusion: Results of this study show that portal hypertension is associated with a poor prognosis; however, some dogs can show prolonged survival. Clinical relevance: Clinical data can guide decision-making for clinicians and owners.

Indicateurs pronostiques chez les chiens atteints d'hypertension portale intra-hépatique. Objectifs: Les principaux objectifs de cette étude rétrospective étaient de décrire une population de chiens souffrant d'hypertension portale secondaire à une maladie hépatique et d'évaluer si le pronostic pouvait être déduit à partir de données historiques, cliniques et clinicopathologiques. Animaux et procédures: Les chiens (N = 76) diagnostiqués avec une hypertension portale intrahépatique entre 2011 et 2020 ont été inclus; les chiens présentant des anomalies hépatiques congénitales connues ont été exclus. L'effet sur la survie a été évalué à l'aide de modèles de risques proportionnels de Cox univariés et multivariés pour les variables historiques, cliniques et clinicopathologiques. Résultats: Les chiens ont survécu pendant une durée médiane de 14 jours (intervalle : 0 à 2028 jours), 31,6 % ayant été euthanasiés dans les 2 jours suivant le diagnostic et 23,7 % ayant survécu plus de 2 mois. La présence d'ictère et la durée des signes cliniques, exprimées en jours, étaient significativement associées au résultat de l'analyse univariée (HR = 1,846, IC à 95 % : 1,094 à 3,117, P = 0,02; HR = 0,995, IC à 95 % : 0,990 à 1,000, P = 0,033, respectivement). Cependant, seule la présence d'ictère était significativement associée à un risque accru de décès dans l'analyse multivariée. Conclusion: Les résultats de cette étude montrent que l'hypertension portale est associée à un mauvais pronostic; cependant, certains chiens peuvent montrer une survie prolongée. Pertinence clinique: Les données cliniques peuvent guider la prise de décision des cliniciens et des propriétaires.(Traduit par Dr Serge Messier).

Whole genome resequencing and custom genotyping unveil clonal lineages in 'Malbec' grapevines (Vitis vinifera L.).

Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

Prevalence and risk factors for hyperthyroidism in Irish cats from the greater Dublin area.

BACKGROUND: Hyperthyroidism is common in older cats. Prevalence varies geographically, but is anecdotally considered low in Ireland. The aim of this study was to document prevalence of hyperthyroidism in older cats in the greater Dublin area of Ireland and to assess environmental and clinical associations for development and identification of the disease. METHODS: Primary-care veterinary practices were requested to select cats aged 10 years or older where blood sampling was being performed for health screening or clinical investigations. Surplus serum/plasma samples were submitted to University College Dublin Diagnostic Endocrine Laboratory for total thyroxine (T4) measurement. Cats were classified as hyperthyroid, equivocal or euthyroid based on a total T4 concentration (reference interval, 15-60 nmol/L), of >60 nmol/L, 30-60 nmol/L or <30 nmol/L, respectively. Simultaneous free T4 or repeat (after 4-6 weeks) total T4 measurement was recommended in all equivocal cases. Animals receiving treatment for hyperthyroidism were excluded. A questionnaire completed by the client and veterinarian detailing historical and physical information was also required. Associations between categorical variables were analysed by Chi-square or Fisher's exact test and odds ratio (OR) calculated. A P value of <0.05 was considered statistically significant. RESULTS: Samples were submitted from 507 cats including 107 (21.1%) hyperthyroid, 54 (10.6%) equivocal and 346 (68.2%) euthyroid. The presence of goitre (P < 0.0001), tachypnoea (P = 0.0378), tachycardia (P = 0.002), polyphagia (P = 0.0003) and weight loss (P < 0.0001) were significantly associated with hyperthyroidism. Cats with goitre were more likely to be diagnosed as hyperthyroid [OR 2.85, (95% CI 1.75-4.62] compared to those without. However, goitre was only palpated in 40 of 102 (39.2%) hyperthyroid cats. Increasing age was the only significant (P < 0.002) risk factor for development of hyperthyroidism. A relationship between hyperthyroidism and sex, breed, lifestyle, parasite control, vaccination status or feeding habits was not identified. CONCLUSIONS: Hyperthyroidism is not uncommon in Irish cats. Age was the only significant risk factor for its development. The high proportion of hyperthyroid cats without palpable goitre (> 60%) may reflect failure to detect goitre and account for the perceived low prevalence of this condition in Ireland.

Periaortic lymphoma in a cat.

CASE SUMMARY: A 14-year-old neutered male Siamese cat was presented with a 3 month history of lethargy, inappetence, dehydration, hindlimb ataxia and intermittent proprioceptive deficits in the hindlimbs. Physical examination revealed low body condition score (1.75/5), pallor and bilateral basilar grade II/VI systolic heart murmur. Neurological examination revealed hindlimb ataxia, severe atrophy of the hindlimb musculature, intermittent hindlimb proprioceptive deficits and normoreflexia. Clinicopathological investigations revealed non-regenerative anaemia (haematocrit 0.17 l/l; reference interval [RI] 0.24-0.45 l/l) and increased feline pancreatic lipase concentration (Spec fPL test [IDEXX] 8.3 µg/l; RI 0.1-3.5 µg/l). Feline leukaemia virus antigen and feline immunodeficiency virus antibody tests were negative. Thoracic and abdominal imaging revealed a soft tissue structure in the area of the thoracoabdominal aorta. CT confirmed a periaortic contrast-enhancing mass extending from the level of T9-L2, with associated intervertebral infiltration at the level of T11-T12. Post-mortem examination confirmed the presence of a solid, white, multinodular, well-demarcated mass encircling the aorta extending from T9-L2. Based on histopathology and immunohistochemistry, a diagnosis of B-cell lymphoma was made. Lymphoma was also identified histopathologically within the kidneys and spleen. Evidence of mild Wallerian degeneration was present within the spinal cord, indicating compression at the level of the periaortic mass. RELEVANCE AND NOVEL INFORMATION: To our knowledge, this is the first report of periaortic lymphoma in the cat. Although periaortic tumours are exceptionally rare in veterinary medicine, lymphoma should be considered as a differential in cats.