The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species

Abstract

Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.

Figure 1

A. littoralis chloroplast genome map. Genes shown inside the circle are transcribed clockwise, whereas genes outside are transcribed counterclockwise. The light gray inner circle shows the AT content, the dark gray corresponds to the GC content.

Figure 2

Simple sequence repeats (SSR) in the A. littoralis cp genome. (A) Frequency of identified SSR types. (B) Number of different identified SSR motifs.

Figure 3

Codon usage patterns analysis of the A. littoralis chloroplast genome. (A) Frequency analysis of amino-acids in A. littoralis cp protein-coding genes. (B) RSCU values of 20 amino acid and stop codons in all protein-coding genes of the A. littoralis cp genome.

Figure 4

Comparison of the boundaries between LSC, SSC, and IR regions among the three Aeluropus species cp genomes.

Figure 5

Nucleotide divergence analysis across Aeluropus species cp genomes.

Figure 6

Maximum likelihood and Bayesian inference phylogenetic tree based on complete cp genomes of A. littoralis and related-species within the Poaceae family. Bootstrap and posterior probability support values are indicated above each node.