Comparative Genomic Analysis of Adaptive and Economic Traits Related Genes in Southern Pines
Abstract
Four major Southern pines, Pinus echinata Mill., P. elliottii Engelm., P. palustris Mill.
and P. taeda L. are evolutionarily young and closely related. They have not been
intensely researched except P. taeda. In this study we addressed the questions of exonintron
structure, nucleotide variation and neutrality in adaptive and economic traits
related genes, and phylogenetic relationships between these pines. Using publically
available data in the NCBI databases, we first developed a series of statistical regression
models. We defined functional relationships between the parameters that can be easily
estimated from a small data sample (e.g. mean exon length and exon/gene ratio), and
parameters that are difficult to assess (e.g. number of genes and exons). Second, we
examined the effects of selection upon the set of studied genes in the four pines. We
collected data from individuals representing all four Southern pines and merged them
with previously published data, and applied four neutrality tests: Tajima’s D, McDonald-
Kreitman (MK), Hudson-Kreitman-Aguade (HKA), and synonymous-nonsynonymous
nucleotide substitutions ratio. Finally, we analyzed phylogenetic relationships between the four Southern pines, and with respect to other selected pine species (P. radiata, P.
pinaster and P. sylvestris), for which the nucleotide sequence data orthologous to the
sequences newly generated in this study were available in the NCBI GenBank. We
applied Maximum Parsimony, Maximum Likelihood and Bayesian Inference
approaches.
Based on the statistical models we expect about 13-14 thousand genes in an
organism with the mean exon length of 334.8 bp (like P. taeda). This number could be
higher in plants (20-21 thousand). Furthermore, we identified signatures of selection in
some of the studied genes, and demonstrated that different parts of a gene could be under
different forms of selection. Therefore, the results of the neutrality tests performed at
the entire gene level could be misleading. Finally, using twelve nuclear loci we
confirmed very tight phylogenetic relationships within the subsection Australes, but the
conclusions were not robust. Using two exclusive sets of three genes led to robust but
conflicting results. Therefore, we demonstrated that conclusions about “species” trees
based on “gene” trees may be misleading, especially for closely related species.
Subject
Pinus taedaPinus echinata
Pinus elliottii
Pinus palustris
Australes
Southern pines
exon-intron structure
alternative splicing
neutrality tests
pine phylogeny
Citation
Koralewski, Tomasz E (2010). Comparative Genomic Analysis of Adaptive and Economic Traits Related Genes in Southern Pines. Doctoral dissertation, Texas A & M University. Available electronically from https : / /hdl .handle .net /1969 .1 /ETD -TAMU -2010 -08 -8509.