*2.1. Transcriptome Sequencing and Assembly*

In order to explore the salt tolerant genes of *B. halophila*, six cDNA libraries were constructed from leaves of eight-months-old control plants (untreated) and plants treated with 200 mM of NaCl for 24 h, and sequenced using the Illumina deep sequencing platform. A total of 68,348,352, 75,684,144, 70,510,750, 86,101,536, 77,402,824, and 84,837,142 raw reads were generated by Illumina sequencing, respectively, after adapter sequence and low quality sequences had been removed, a total of 66,834,236, 73,359,338, 69,082,978, 84,155,542, 75,577,004, and 82,931,756 clean reads were obtained, and the Q20 percentage (proportion of nucleotides with a quality value larger than 20) for each data was 96.5%, 96.48%, 96.25%, 96.54%, 96.49%, and 96.45%, respectively. The GC (%) ratio for each library was 46.88%, 47.4%, 47.29%, 47.28%, 47.33% and 47.29% (Table 1). Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with the min\_kmer\_cov set to 2 by default and all other parameters set to default [17]. As a result, a total of 117,091 unigenes with lengths ranging from 201 bp to 15,762 bp were obtained. The size distribution of the unigenes is shown in Figure 1. The size distribution showed that the unigenes ranged from 200 bp to 1 kbp was the majority (Figure 1). The average length, median length, and N50 of the assembled unigenes were 956 bp, 631 bp and 1408 bp, separately. The total length of 117,091 unigenes was 110 Mb, which suggests that most of the sequencing data had been successfully assembled into relatively long unigenes.


**Table 1.** Summary of the sequencing data of the Betula halophila transcriptome. **Sample Raw Reads Clean Reads Clean Bases Error (%) Q20 (%) Q30 (%) GC Content(%)**

**Table 1.** Summary of the sequencing data of the Betula halophila transcriptome.

**Figure 1.** Length distribution of the assembled unigenes. (**A**) The number of contigs with same length. (**B**) The number of contigs with length 200–500 bp, 500 bp−1 kb, 1–2 kb and larger than 2 kb are shown. **Figure 1.** Length distribution of the assembled unigenes. (**A**) The number of contigs with same length. (**B**) The number of contigs with length 200–500 bp, 500 bp−1 kb, 1–2 kb and larger than 2 kb are shown.
