Complete chloroplast genome of Vicia faba L.

The young leaves of V. faba were kindly provided by the Legume Research Department, College of Agricultural and Forestry Sciences, Qinghai University. This species was identified by Xue-Xia WU and is preserved in the Qinghai University, State Key Laboratory of Plateau Ecology and Agriculture. No permission was required for collecting the samples, as they are not included in the list of nationally key protected plants. The samples were collected from well-grown, disease-free, and pest-free fresh leaves, immediately frozen in liquid nitrogen, and subsequently stored in a -80 ℃ refrigerator for spare parts. Total genomic DNA was extracted using a modified cetyltrimethylammonium bromide (CTAB) method. Sequencing libraries were generated using the NEBNext® Ultra™ DNA Library Preparation Kit. After passing the quality of the library, sequencing was performed on the BGI platform to obtain raw data. A total of 86,250,000 paired-end reads, each comprising 150 bp sequences, were generated. Low-quality sequences were filtered out using Fastp v0.23.0 software, and the resulting clean reads were used for subsequent splicing. The paired-end reads of V. faba were filtered and assembled into a complete plastome using and GetOrganelle v1.7.1 with default parameters. The quality of the newly assembled genomes was evaluated on a level basis by aligning the trimmed raw reads to the de novo assemblies using Geneious mapper, Geneious v8.0.2 with medium- to low-sensitivity settings and up to five iterations. The resulting complete chloroplast genomes were automatically annotated using CPGAVAS2 software, followed by manual adjustments. Based on the annotation results, manual corrections of start/stop codons and intron/exon boundaries were performed in Geneious v8.0.2. We attempted to use the online tRNAscan-SE service v2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) to enhance the identification of tRNA genes.