Draft genome sequencing and secretome profiling of Sclerotinia sclerotiorum revealed effector repertoire diversity and allied broad-host range necrotrophy.

White mold commonly known as Sclerotinia sclerotiorum causes stem rot disease and has emerged as one of the major fungal pathogens of oilseed Brassica across the world. In the present study, consistently virulent S. sclerotiorum isolate "ESR-01" was sequenced and an assembly size of ~ 41 Mb with 328 scaffolds having N50 of 447,128 was obtained. Additionally, 27,450 single nucleotide polymorphisms (SNPs) were identified from 155 scaffolds against S. sclerotiorum 1980 isolate, with an average SNP density of ~ 1.5 per kb genome. 667 repetitive elements were identified and approximately comprised 7% of the total annotated genes. The DDE_1 with 454 in numbers was found to be the most abundant and accounts for 68% of the total predicted repetitive elements. In total, 3844 simple sequence repeats are identified in the 328 scaffolds. A total of 9469 protein-coding genes were predicted from the whole genome assembly with an average gene length of 1587 bp and their distribution as 230.95 genes per Mb in the genome. Out of 9469 predicted protein-coding genes, 529 genes were observed encoding the CAZymes (Carbohydrate-Active enzymes) capable of degradation of the complex polysaccharides. Glycosyltransferase (GT) families were most abundant (49.71%) among the predicted CAZymes and GT2 (23%), GT4 (20%), and glycoside hydrolase (GH) 23% with GH18 (11%) were the prominent cell wall degrading enzyme families in the ESR-01 secretome. Besides this, 156 genes essential for the pathogen-host interactions were also identified. The effector analysis in the whole genome proteomics dataset revealed a total of 57 effector candidates (ECs) and 27 of them were having their analogs whereas the remaining 30 were novel ones. Eleven selected ECs were validated experimentally by analyzing the expression profile of the ESR-01 isolate of S. sclerotiorum. Together, the present investigation offers a better understanding of the S. sclerotiorum genome, secretome, and its effector repertoire which will help in refining the present knowledge on S. sclerotiorum-Brassica interactions and necrotrophic lifestyle of the phytopathogen in general.

Comparative fatty acid profiling of Indian seabuckthorn showed altitudinal gradient dependent species-specific variations.

The present study provides the first comparative fatty acid profiling of the three Indian seabuckthorn species, collected from varying altitudes (2900-4300 masl) of Trans-Himalayas (Hippophae rhamnoides, H. tibetana) and Sikkim Himalayas (H. salicifolia) regions. Gas chromatography-mass spectrometry analysis showed variability in fatty acid composition of different seabuckthorn populations. Sikkim populations showed higher (1.28-1.6 folds) palmitic acid than Trans-Himalayan populations which possess higher linoleic (1.3-1.5 folds) and linolenic (1.6-1.8 folds) acids. Interestingly, a strong altitudinal gradient associated positive correlation was observed with the degree of unsaturation and PUFA content while negative correlation was observed with saturated fatty acids content of different seabuckthorn populations. H. salicifolia collected from Sikkim showed healthy ω-6:ω-3 ratio (closer to 1:1) of functional lipids exhibiting its better nutraceutical potential than other commonly used seed oils. Interestingly, H. tibetana from Losar showed higher (5.81) degree of unsaturation than Sikkim populations (3.5) suggesting its better stress tolerance trait. Chemo-taxonomic diversity analysis also formed two broad clusters of Trans-Himalayan and Sikkim populations which correlated with earlier taxonomic studies.

Puroindoline allelic diversity in Indian wheat germplasm and identification of new allelic variants.

Grain hardness is an important quality trait that influences product development in wheat. This trait is governed by variation in puroindoline proteins (PINA and PINB). Our study evaluated 551 Indian wheat germplasm lines for diversity in Pina and Pinb genes. Eighty-two lines were shortlisted for full length sequencing and grain hardness studies. Sequencing studies identified six unknown alleles: two for the Pina gene and four for the Pinb gene. Five of them were novel with non-synonymous changes in the corresponding amino acid sequences. Identified mutations in the deduced mature proteins and their pre- and pro-peptides influenced the hardness characteristics of the grain. We classified these 82 varieties into different hardness categories with reference to international and Indian systems of classification. The majority of Indian wheat varieties were categorized as hard. This study revealed that unexplored Indian wheat germplasm can be a good source of genetic variability for both Pina and Pinb genes, helping in marker-assisted breeding and in obtaining wheat with different textural properties.