Supporting data for "Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis"

The woody halophyte <i>Tamarix chinensis</i> is a pioneer tree species in the coastal wetland ecosystem of Northern China, exhibiting high resistance to salt stress. However, the genetic information underlying salt tolerance in <i>T. chinensis</i> remains to be seen. Here we present a genomic investigation of <i>T. chinensis</i> to elucidate the underlying mechanism of its high resistance to salinity. <br>Using a combination of PacBio and high-throughput chromosome conformation capture data, a chromosome-level <i>T. chinensis</i> genome was assembled with a size of 1.32 Gb and scaffold N50 of 110.03 Mb. Genome evolution analyses revealed that <i>T. chinensis</i> significantly expanded families of <i>HAT</i> and <i>LIMYB</i> genes. Whole-genome and tandem duplications contributed to the expansion of genes associated with the salinity adaptation of <i>T. chinensis</i>. Transcriptome analyses were performed on root and shoot tissues during salt stress and recovery, and several hub genes responding to salt stress were identified. <i>WRKY33/40, MPK3/4</i>, and <i>XBAT31</i> were critical in responding to salt stress during early exposure, while <i>WRKY40, ZAT10, AHK4, IRX9</i>, and <i>CESA4/8</i> were involved in responding to salt stress during late stress and recovery. In addition, <i>PER7/27/57/73</i> encoding class III peroxidase and <i>MCM3/4/5/7</i> encoding DNA replication licensing factor maintained up/downregulation during salt stress and recovery stages. <br>The results presented here reveal the genetic mechanisms underlying salt adaptation in <i>T. chinensis</i>, thus providing important genomic resources for evolutionary studies on tamarisk and plant salt tolerance genetic improvement.