Genomic characteristics and phylogenetic analysis of chloroplasts in Sorghum sudanense

In order to determine the sequence characteristics of the chloroplast genome of Sorghum sudanense and establish its systematic position in the Sorghum genus, we sequenced the chloroplast genome of S. sudanense using the DNBSEQ-T7 sequencing platform, and analyzed its gene composition, simple-sequence repeats, long repeat sequences, and inverted repeat (IR) region boundary structure; constructed neutral, ENC, and PR2 plots; and examined its systematic evolution. The results revealed that the chloroplast genome of S. sudanense has a typical tetrad structure, with a length of 140 754 bp, comprising 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, although lacks the typical ccD and ycf1 genes. In addition, we detected a total of 27 simple-sequence repeats (SSRs) and 47 long repeat sequences (long repeats). The numbers of nucleotide polymorphisms in the long single-copy (LSC) and small single-copy (SSC) regions were found to be significantly higher than those in the (IR) region, with the variability in the LSC region being greater than that in the SSC and IR regions. The variation of nucleotide diversity (Pi) ranged from 0 to 0.01852, and on the basis of Pi, we selected 10 high variation regions (≥ 0.01215), all of which were located in the LSC region. Furthermore, we detected differences in GC contents at different codon positions in the chloroplast genomes of S. sudanense and 11 related species, with a preference for ending with A/U, and with an average ENC value of 47.50, indicating a weak codon bias. The main factor affecting codon usage bias in these 12 species was natural selection, with less influence from internal mutation pressure. There were a total of 15 optimal codons in Sudan grass chloroplast genes (CAA, AAA, UUU, UAU, AUU, UAA, GCA, CCA, ACU, GUA, AGA, CGA, CUU, UCC, and UCU), all ending in an A or U base. Moreover, we detected a relatively close genetic relationship between S. sudanense and S. bicolor subsp. drummondii. Our findings in this study, will provide a reference for the development of molecular markers, assessment of genetic diversity, and further research on the conservation biology and population genetics of sorghum plants.