*3.2. De Novo Assembly, Functional Annotation, and Classification*

Transcriptome sequencing was carried using an Illumina HiSeq 4000 platform (Beijing Novogene Biological Information Technology Co., Ltd., Beijing, China); clean reads were used for de novo assembly using Trinity (version: trinityrnaseq-r20131110) with the default parameters to obtain transcripts, and TGICL version 2.1 software was used to cluster the transcripts into unigenes [48,49]. For functional prediction and classification, all unigenes were compared against public databases, including NCBI non-redundant protein sequences (Nr), Nt, Protein Family (Pfam), Eukaryotic Orthologous Groups of Proteins (KOG/COG), Swiss-Prot, the KEGG Orthology database (KO), and Gene Ontology (GO). BLAST [50] was used for unigene annotation in the Nt, Nr, COG, and Swiss-Prot databases. The

KEGG Automatic Annotation Server [51] was used for KEGG annotation of unigenes. Blast2GO [52] and Nr annotation results were used for the GO annotation.


**Table 6.** The location and habitat of the 6 *L. yunnanensis* populations.
