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Asparagus cochinchinensis is a traditional Chinese medicinal plant. The chloroplast (cp) genome study on A. cochinchinensis is poorly understood. In this research, we collected the data from the cp genome assembly and gene annotation of A. cochinchinensis, followed by further comparative analysis with six species in the genus Asparagus. The cp genome of A. cochinchinensis showed a circular quadripartite structure in the size of 157,095 bp, comprising a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions. A total of 137 genes were annotated, consisting of 86 protein-coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 5 pseudo-genes. Forty scattered repetitive sequences and 247 simple sequence repeats loci were marked out. In addition, A/T-ending codons were shown to have a basis in the codon analysis. A cp genome comparative analysis revealed that a similar gene composition was detected in the IR and LSC/SSC regions with Asparagus species. Based on the complete cp genome sequence in Asparagaceae, the result showed that A. cochinchinensis was closely related to A. racemosus by phylogenetic analysis. Therefore, our study providing A. cochinchinensis genomic resources could effectively contribute to the phylogenetic analysis and molecular identification of the genus Asparagus.

Asparagus setaceus (Kunth) Jessop is a horticultural plant of the genus Asparagus. Herein, the whole chloroplast (cp) genome of A. setaceus was sequenced with PacBio and Illumina sequencing systems. The cp genome shows a characteristic quadripartite structure with 158,076 bp. In total, 135 genes were annotated, containing 89 protein-coding, 38 tRNA, and 8 rRNA genes. Contrast with the previous cp genome of A. setaceus registered in NCBI, we identified 7 single-nucleotide polymorphisms and 15 indels, mostly situated in noncoding areas. Meanwhile, 36 repeat structures and 260 simple sequence repeats were marked out. A bias for A/T-ending codons was shown in this cp genome. Furthermore, we predicted 78 RNA-editing sites in 29 genes, which were all for C-to-U transitions. And it was also proven that positive selection was exerted on the rpoC1 gene of A. setaceus with the K a/K s data. Meanwhile, a conservative gene order and highly similar sequences of protein-coding genes were revealed within Asparagus species. Phylogenetic tree analysis indicated that A. setaceus was a sister to Asparagus cochinchinensis. Taken together, our released genome provided valuable information for the gene composition, genetics comparison, and the phylogeny studies of A. setaceus.