Distribution of genes

From Purdue Genomics Database Facility

S. moellendorffii genes are compressed in small gene rich regions while large deserts of genes are retaind

T. Nishiyama (tomoakin@kenroku.kanazawa-u.ac.jp)

To explore how S. moellendorffii could have a very small genome, various size measurements were compared among P. patens, S. moellendorffii, and A. thaliana. As a results, introns, and 3' UTR is shorter in S. moellendorffii, while CDS size were retained as large as A. thaliana. These comparison suggests that the S. moellendorffii underwent an evolution to reduce the total genome size and only the CDS which was functionally constrained to shorten were retained in size. Although the measurement of 5' UTR might be inaccurate due to different cDNA library construction methods, the peak location is consistent with the hypothesis.

Although the total genome size is small, S. moellendorffii genome seems to have large repeats with little gene content.

Instead, the gene rich regions are very tightly compressed with little inter-genic region.

To discribe the situation, quantitatively, I calculated gene distance between neighboring genes based on the gff files, as

distance = (this transcript start) - (previous transcript end)

the distribution of the distance was calculated for S. moellendorffii Filtered Model 2 dataset and P. patens Filtered model dataset.

The summary of the statistices were

statistics	S. moellendorffii	P. patens	A. thaliana
Min	-33074	-17007	-9065
1st Qu.	393	1647	309
Median	1086	4916	904
3rd Qu.	3038	13913	2190
Max	275050	272201	497963
Mean	4139	10524	2221

The data show that usual inter genic regions are more than 4-fold smaller compared to P. patens, though the mean are less impacted because there are very large deserts of gene and maximum are larger in S. moellendorffii. The distribution in S. moellendorffii looks similar to A. thaliana. However, the above calculation reflects the effort to clone full-length cDNA and identify the UTR in A. thaliana. A similar comparison between the CDS were performed

statistics	S. moellendorffii	P. patens	A. thaliana
Min	-32950	-8229	-4556
1st Qu.	445	1812	1363
Median	1158	5063	2696
3rd Qu.	3119	14055	4732
Max	275050	272201	501725
Mean	4139	10672	3993

This comparison shows that the averege distance represented by 1st quatinent median and 3rd quatinent is smallest in S. moellendorffii and A. thaliana is intermediate.

Speculations

The skew in the pattern of intergenic regions might suggest that the selective force to reduce the genomesize, whatever the nature may be (which is unclear), act on euchromatin region easier than heterochromatin region. Or, the heterochromatin are more stable in some regard and euchromatin are more easily attacked.

Note: Negative number of distance, indicates there are overlapping transcripts predicted. The extremely large negative ones seems as results of selection of overlapping gene models that are not likely a good ones.

S. moellendorffii genes have smaller untranslated regions and introns, while the CDS size is not smaller

The size of 5' and 3' untranslated regions of P. patens and S. moellendorffii were calculated based on the start, and stop codon annotation and the exon annotations of each gene on the GFF files. For arabidopsis, the five_prime_UTR and three_prime_UTR features were used. The size of cds were calculated by summing up the size of CDS features belonging to each gene. 0 length UTR were assumed to mean that they are undetermined and removed.

For the CDS comparison, when the total annotation data were used, the pattern in P. patens showed a strange peak around 400 bp, and the shape seemed different from S. moellendorrfii and A. thalina. Since this was suspected to come from errornous annotation or transposon associated gene fragment, a comparison of CDS of actively transcribed gene were performed by using only the CDS data that is associated with 3' UTR annotation. Because 3' UTR is usually identified from EST data this should have restricted to actively transcribed gene.

statistics	S. moellendorffii	P. patens	A. thaliana
Min	1	1	1
1st Qu.	37	117	57
Median	116	236	100
3rd Qu.	396	445	175
Max	275050	272201	501725
Mean	347	393	139

statistics	S. moellendorffii	P. patens	A. thaliana
Min	150	150	51	150 is perhaps the cut-off of the annotation and not biologically meaningful
1st Qu.	684	528	597
Median	1071	873	1041
3rd Qu.	1557	1440	1557
Max	25390	14670	16010
Mean	1276	1137	1211

statistics	S. moellendorffii	P. patens	A. thaliana
Min	150	156	51
1st Qu.	800	708	666
Median	1209	1158	1080
3rd Qu.	1737	1749	1578
Max	25390	14580	16010
Mean	1445	1404	1255

statistics	S. moellendorffii	P. patens	A. thaliana
Min	1	1	1
1st Qu.	79	223	151
Median	143	351	205
3rd Qu.	302	520	269
Max	7840	7901	3118
Mean	308	459	227

statistics	S. moellendorffii	P. patens	A. thaliana
Min	0	0	1
1st Qu.	52	137	86
Median	58	206	99
3rd Qu.	72	323	166
Max	48860	42110	10234
Mean	58	206	164