Analysis of the complete chloroplast genome sequence characteristics and code usage bias of Sorghum bicolor × Sorghum sudanense hybrid

High-throughput sequencing of the leaves of a Sorghum bicolor × S. sudanense hybrid was performed, its chloroplast genome was assembled, its gene and sequence characteristics were annotated and analyzed, and its phylogenetic tree based on the shared coding gene sequences was constructed. The results showed that the chloroplast genome size of the S. bicolor × S. sudanense hybrid was 140 643 bp and total GC content was 38.48%. The lengths of the large single copy region (LSC), small single copy region (SSC), and the reverse complementary repeat region (IR) were 82573, 12506, and 22 782 bp, respectively. Furthermore, the results showed that the chloroplast genome of S. bicolor × S. sudanense hybrid contains 132 genes, and the number of protein coding genes, tRNA genes, and rRNA genes was 86, 38, and 8, respectively, with missing accD and ycf1 genes. A total of 31 simple sequence repeats (SSRs) and 42 long repeat sequences (longrepeats) were detected. SSRs were mainly single nucleotide repeats of A or T bases, whereas longrepeats were mainly palindrome repeats. The overall variability of the LSC region was higher, followed by that of the SSC region, with the IR region having the lowest variability. The codon usage bias in the chloroplast genome of S. bicolor × S. sudanense hybrid was mainly influenced by natural selection and is less affected by internal mutation pressure. There were 15 optimal codons (CAA, AAA, UUU, UAU, AUU, UAA, GCA, CCA, ACU, GUA, AGA, CGA, CUU, UCC, and UCU), all ending with A and U. S. bicolor × S. sudanense hybrid is closely related to S. bicolor.