Biology subjects

Stevanato, P.

Publications and source records attributed to Stevanato, P..

3 recordsLinked to original sources

bioRxiv2024

Plant phenotypic differentiation outweighs genetic variation in shaping the lettuce leaf microbiota

Lettuce is a widely consumed raw vegetable, making it crucial to understand and predict its leaf-associated microbial communities for the benefit of both plant and human health. While environmental factors are known to strongly influence plant leaf microbiomes, the role of plant-specific determinants in shaping microbial diversity remains unclear. In this study, we investigated the impact of three key plant factors -genetic distance, morphology and leaf micro- and macronutrient content- on the composition and diversity of lettuce leaf bacterial communities. Using 131 fully-sequenced Lactuca sativa genotypes, we analyzed their leaf-associated bacterial communities via 16S rRNA amplicon sequencing. Our findings revealed that morphological classification, as defined by breeders, exerts a greater influence on bacterial community diversity than genetic distance or variations in leaf nutrient levels. Together with shoot traits they explained 13.9% of the observed bacterial diversity. Further analysis of 10 specific leaf morphological traits showed that heart formation, head height, and venation types significantly shaped bacterial richness and evenness, mainly acting on non-hub members. The strong association between leaf morphology and bacterial community structure suggests that phenotypic traits play a disproportionately large, yet understudied, role in leaf microbiota establishment offering new potential for manipulation by breeders.

plant biology↗

bioRxiv2020

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

A contiguous assembly of the inbred EL10 sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short read error correction. The EL10.1 assembly was 540 Mb, of which 96.7% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNAseq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals drawn from EL10 progeny and three unrelated germplasm accessions, producing estimates from 633 to 875 Mb/1C. Read depth mapping with short-read whole genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.

genomics↗

bioRxiv2020

Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

genomics↗