HaplotypeCaller was used to estimate the SNPs and indels for putative diploids using the default parameters. The distribution of calling depths (DP) of each raw variant was estimated as a criterion for variant filtering to reduce false positives. Low depths and repetitive variants were removed from...
The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including bot
The long-term effects of the olive mill wastewater (OMWW) spreading on soil chemical properties, microbial community, and olive tree parameters have been far poorly investigated. Therefore, this study aims to evaluate the effect of OMWW application on an
raw sequence data were imported into QIIME2 manually using the “qiime tools import” command. The quality trimming, denoising, merging and chimera detection and non-singleton amplicon sequence variants (ASVs) grouping were done using
To estimate the kinship among samples, TASSEL (v5.0)103 was used to calculate the kinship matrix. Based on the SNPs, trait values and kinship matrix, we used the FarmCPU model to perform a GWAS with GAPIT (v3.0)104. The population structure in the GWAS was estimated in GAPIT with the ...
the transcriptomes of these cell types of virgin RY7-33-97 rubber trees were sequenced using the Illumina paired-end sequencing method with three biological replicates. Totally six RNA-seq libraries were generated and more than 312 million raw reads were obtained. After trimming adaptors and removin...