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Abstract
Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in ‘responses to stress’, ‘ubiquitin-dependent protein catabolic processes’, and ‘biological regulation’. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats.
Highlights
Evolved genes with a higher divergence than the remaining pairs of genes during recent speciation of closely related species are assumed to be responsible for differentiated habitat adaptation [1,2,3]
We cultured P. pruinosa calli using the method described by Zhang et al [25] under the same conditions with P. euphratica, replaced the growth medium of one set with fresh, unamended medium and that of another set with fresh medium supplemented with 100 mM NaCl, and harvested both sets 24 h later
Based on the log 2 ratio value, we found that only one pair of the orthologous expressed sequence tags (ESTs) (Unigene56801_All and Unigene25389_All in P. euphratica and P. pruinosa, homologous to Arabidopsis Proteinase inhibitor I4, serpin) has a higher expression level in salt-stressed callus when compared with control callus in both P. euphratica and P. pruinosa
Summary
Evolved genes with a higher divergence than the remaining pairs of genes during recent speciation of closely related species are assumed to be responsible for differentiated habitat adaptation [1,2,3] Some of these genes may be companied by changed spatial and temporal expressions [4,5] possibly due to their critical mutations [5]. ‘ generation’ sequencing provides an opportunity to obtain abundant and inexpensive genomic data for non-model species, especially transcriptome sequences [10,13] Such sequences are being used to detect genes showing rapid evolution in the recent past across the entire genomes [12,14,15,16,17]
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