| Summary: | <i>Tamarix</i> spp. (saltcedar) were introduced from Asia to the southern United States as windbreak and ornamental plants and have spread into natural areas. This study determined differential gene expression responses to water deficit (WD) in seedlings of <i>T. chinensis</i> and <i>T. ramosissima</i> from established invasive stands in New Mexico and Montana, respectively. A reference de novo transcriptome was developed using RNA sequences from WD and well-watered samples. Blast2GO analysis of the resulting 271,872 transcripts yielded 89,389 homologs. The reference <i>Tamarix</i> (Tamaricaceae, Carophyllales order) transcriptome showed homology with 14,247 predicted genes of the <i>Beta vulgaris</i> subsp. <i>vulgaris</i> (Amaranthaceae, Carophyllales order) genome assembly. <i>T. ramosissima</i> took longer to show water stress symptoms than <i>T. chinensis.</i> There were 2068 and 669 differentially expressed genes (DEG) in <i>T. chinensis and T. ramosissima,</i> respectively; 332 were DEG in common between the two species. Network analysis showed large biological process networks of similar gene content for each of the species under water deficit. Two distinct molecular function gene ontology networks (binding and transcription factor-related) encompassing multiple up-regulated transcription factors (MYB, NAC, and WRKY) and a cellular components network containing many down-regulated photosynthesis-related genes were identified in <i>T. chinensis</i>, in contrast to one small molecular function network in <i>T. ramosissima</i>.
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