Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.
Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, ower and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identi cation and phylogenetic studies. Next generation sequencing has revolutionized the approaches for discovery, assessment and validation of molecular markers. We conducted a genome wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data.By performing in silico mining of microsatellite repeat-motifs, we developed 45,066 perfect SSR markers. Of which 203 markers were successfully validated and 101 (49.75%) polymorphic primer pairs were utilized for an in depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6% and 4.3% of di-, penta-and hexa-nucleotide repeats in the bottle gourd genome. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%) and 11 watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery and for breeding in bottle gourd and other cucurbits species. Key MessageDevelopment of 45,066 perfect microsatellite markers as a valuable tool for marker assisted selection (MAS) in plant breeding.
Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance,informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding geneticimprovement, cultivar identification and phylogenetic studies. Next generation sequencing has revolutionizedthe approaches for discovery, assessment and validation of molecular markers. We conducted a genome wideanalysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data.By performing in silico mining of microsatellite repeat-motifs, we developed 45,066 perfect SSR markers. Ofwhich 203 markers were successfully validated and 101 (49.75%) polymorphic primer pairs were utilized for anin depth genetic diversity and population structure analysis of 96 accessions from the National Genebank ofIndia. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%),further 21.03%, 9.6% and 4.3% of di-, penta- and hexa- nucleotide repeats in the bottle gourd genome. Syntenyof SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber(93.2%), 12 chromosomes of melon (87.4%) and 11 watermelon (90.8%). The generated SSR markers providea valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, genediscovery and for breeding in bottle gourd and other cucurbits species.
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