Intron losses and gains in the nematodes

Biology Direct

Table 1 Relationships among the frequencies of intron losses and intron gains, and genomic characteristics in 104 nematodes species

y	x	Slope	P	P_BH	R²
Intron losses	Intron gains	0.712	5 × 10⁻¹⁵	6 × 10⁻¹⁴	0.4485
	Intron density	− 7.207	0.001	0.004	0.0914
	Genome size	− 0.029	0.540	0.669	− 0.0061
	CDS length	− 0.036	0.024	0.061	0.0399
	Exon length	− 0.004	0.986	0.986	− 0.0098
	Intron length	− 0.043	0.479	0.650	− 0.0048
	Coding gene number	0.000	0.817	0.885	− 0.0093
	Total intron number	− 0.002	0.041	0.089	0.0308
Intron gains	Intron density	− 4.761	0.012	0.039	0.0509
	Genome size	0.004	0.921	0.958	− 0.0097
	CDS length	− 0.035	0.025	0.061	0.0388
	Exon length	− 0.289	0.143	0.286	0.0113
	Intron length	0.026	0.594	0.702	− 0.0070
	Coding gene number	0.000	0.500	0.650	− 0.0053
	Total intron number	− 0.001	0.218	0.354	0.0052
Intron density	Genome size	0.005	0.026	0.061	0.0383
	CDS length	0.004	6 × 10⁻¹¹	5 × 10⁻¹⁰	0.3376
	Exon length	− 0.053	10⁻⁷	7 × 10⁻⁷	0.2359
	Intron length	0.002	0.491	0.650	− 0.0051
	Coding gene number	10⁻⁵	0.167	0.310	0.0091
	Total intron number	4 × 10⁻⁴	< 2 × 10⁻¹⁶	5 × 10⁻¹⁵	0.6234
Genome size	CDS length	0.028	0.376	0.575	− 0.0020
	Exon length	− 0.230	0.662	0.748	− 0.0079
	Intron length	0.483	2 × 10⁻⁴	0.001	0.1158
	Coding gene number	0.002	9 × 10⁻⁷	5 × 10⁻⁶	0.2037
	Total intron number	0.002	0.209	0.354	0.0058

The relationships were analyzed using phylogenetic generalized least squares analysis. The phylogenetic signals (λ) are 0.99 (p = 2.4 × 10⁻¹⁴), 0.95 (p = 1.9 × 10⁻⁵), 1.00 (p = 5.6 × 10⁻⁴⁶), 1.00 (p = 3.4 × 10⁻²³), 0.82 (p = 5.0 × 10⁻¹⁴), 1.00 (p = 2.1 × 10⁻⁵⁴), 1.00 (p = 2.7 × 10⁻⁴⁷), 0.54 (p = 7.6 × 10⁻⁸), and 0.97 (p = 1.4 × 10⁻³²) for intron losses, intron gains, scaled intron density (intron density), genome size, the median length of protein coding sequences (CDS length), the median length of exon (exon length), the median length of intron (intron length), coding gene number, and total intron number, respectively. Except for the genome size, these traits were calculated from the 1577 orthologs of each genome. P and R², the p-value and adjusted R-squared obtained in phylogenetic generalized least squares analysis.; P_BH, the p-value adjusted by Benjamini–Hochberg

ISSN: 1745-6150