Decoding the Ascaris suum Genome using Massively Parallel Sequencing and Advanced Bioinformatic Methods e Unprecedented Prospects for Fundamental and Applied Research - Ascaris: The Neglected Parasite - page 280

TABLE 11.1 Some salient features of the Ascaris suum genome
Estimated genome size in megabases 309

Total number of base pairs (bp) within assembled scaffolds 272,782,664

N50 length in bp; total number 2 kb in length 407,899; 1618

>

N90 length in bp; total number N90 length 80,017; 748

>

GC content (%) of whole genome 37.9

Repetitive sequences (%) 4.4

Proportion (%) of genome that is coding (exonic; including introns) 5.9; 44.2

Number of putative coding genes 18,542

Gene size (mean bp) 6536

Average coding domain length (mean bp) 983

Average exon number per gene (mean) 6

Gene exon length (mean bp) 153

Gene intron length (mean bp) 1081

GC content (%) in coding regions 45

Number of transfer RNAs 255

with experimental data available for homologous genes in model
organisms, such as Caenorhabditis elegans ( www.wormbase.org ) and
Drosophila melanogaster ( www.flybase.org ) . In a prokaryotic organism
identifying coding genes, which lack introns, is often based on the
prediction of long open reading frames (ORFs), followed by a homology-
based inference of function. This process can be enhanced based on codon
usage and/or AT-richness using pattern predictive modeling (e.g. Hidden
Markov Modeling, HMM). 20 However, generally, a simple ORF prediction
will, at least, provide an acceptable draft annotation. For eukaryotic
genomes, in which intronic regions can be tens of kilobases or longer in
length, such an approach is not possible. Predictive modeling based on
codon usage, AT-richness, and intron-exon boundary “splice” signal
sequences is required using various algorithms. 21 Most programs use
a training set of well-defined transcripts to initiate and then drive the
modeling process. Therefore, for A. suum , we isolated total RNAs from
third-stage larvae (L3s) from eggs ( n

¼

500,000), L3s migrating through

liver parenchyma ( n

¼

60,000) or lungs ( n

¼

80,000) or fourth-stage larvae

(L4s) from the small intestine ( n 30,000) as well as from the somatic

musculature or reproductive tracts from two individual adult males and
two adult females. Messenger RNAs were purified using polyadenylated

¼