Improved Ascaris gene models, alternative splicing, and RNA expression profiles. (A) Improved Ascaris gene models. Illustrated is a genome browser locus view for selected RNA-seq tracks and a comparison of gene models defined in previous papers (Jex et al. 2011; Wang et al. 2012) and here defined with a gene prediction program (AUGUSTUS) (Stanke et al. 2006) and with new RNA-seq data (Current Gene Models) (see Supplemental Material). Comprehensive RNA-seq data from 25 different developmental stages were used to refine Ascaris gene models. (B) Refined and new gene models. Comparison of the gene models between previous studies and the current version reveals that (1) many previously defined independent genes correspond to single genes and have been merged in the current genome annotations, and (2) an additional approximately 5500 (30%) new genes were identified and annotated in our revision. (C) Alternative splicing in Ascaris and Parascaris. Alternatively spliced isoforms were identified using comprehensive RNA-seq data sets in Ascaris and Parascaris (see Supplemental Material). (D) Ascaris developmental RNA expression profiles. The heatmap illustrates the dynamic expression of 10,874 genes (with average RPKM ≥5 or max RPKM ≥20) across the 25 different developmental stages of Ascaris (see Supplemental Material), including regions of the male germline (1, mitotic region; 2, spermatogenesis; 3, post-meiotic region; 4, seminal vesicle; and 5, spermatids), regions of the female germline (1, mitotic region; 2, early pachytene; 3, late pachytene; 4, diplotene; and 5, oocyte), zygote maturation stages prior to pronuclear fusion isolated from the uterus (z1-4) (see Wang et al. 2014), early development stages (1c, 1-cell [24 h of development at 30°C]; 2c, 2-cell [46 h]; 4c, 4-cell [64 h]; 16c, 16-cell [96 h]; 5d, 5-day [32–64 cells]; and 7 d, 7-d [about 256 cells]), larvae (L1 and L2), and adult somatic tissues. (Mu) Muscle; (In) intestine; (Ca) carcass, which includes the cuticle, hypodermis, muscle, nervous system, and pharynx.
