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Next, we aligned the reference and repaired sequence to the reads of each barcode by bowtie (version 1.1.2, http://bowtie-bio.sourceforge.net/index.shtmL) with no mismatch.

Gene expression values were normalized based on the total number of uniquely mapped reads of each library.

The most differentially expressed contigs were selected after firstly normalising the reads of each strain to the total reads number.

Except for the cold stressed library (ZJ-COLD), the sequenced reads of each population are approximately the same (∼8,500,000 reads).

We examined bases from sequencing reads of each NGS platform.

In those cases, the reads of each contig was counted only one time.

Unmapped reads of each sample were assembled independently from the reference.

The reads of each transcript belonging to the same pathway were summed up.

High quality reads of each sample were remapped to transcripts to estimate the abundance of transcripts.

The Q20 bases rate of reads of each individual is above 90%.

On average, 2000332 high quality reads of each sample were obtained with high evenness.

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