Features of the S. grijsii chloroplast genomes
The total length of the chloroplast genome of S. grijsii is 158,591 bp, containing a large single-copy region (LSC), a small single-copy region (SSC) and a pair of inverted repeat sequences (IRa and IRb) with lengths of 88,046 bp, 18,409 bp and 52,136 bp, respectively. The Guanine (G) and Cytosine (C) content in the whole chloroplast genome was 37.0% (see Table 1 and Fig. 1). It contains 129 genes with different functional classifications, including 84 genes encoding proteins, 37 tRNA genes, and eight rRNA genes.
Table 1
Detail characteristics of the chloroplast genome of S.grijsii.
Category | Item | Description |
Structure of cp genome | Large single copy(LSC) | 88046 bp |
| Small single copy (SSC) | 18409 bp |
| A pair of inverted repeats (IRs) | 52136 bp |
| The whole length of the cp genome | 158591 bp |
Gene composition | Total number of genes | 129 |
| Coding genes | 84 |
| tRNAs | 37 |
| rRNAs | 8 |
| Number of genes in large single-copy region | 84 |
| Number of genes in small single-copy region | 13 |
| Number of genes in the inverted repeat region | 18 |
GC content | GC content of large single-copy region | 34.8% |
| GC content of small single-copy region | 30.9% |
| Inverse repeat GC content | 42.7% |
| Average GC content | 37.0% |
Single nucleotide content | A | 35.5% |
| T | 23.7% |
| C | 19.4% |
| G | 21.4% |
SSR analysis of S. grijsii chloroplast genome
Eighty-four SSR loci were detected, in the S. grijsii chloroplast genome, with an average length (total SSR length/total SSR count) of 11.34 bp. Of which 60 were mononucleotides, 2 were dinucleotides, 8 were trinucleotides, 13 were tetranucleotides, 1 was a pentanucleotide, and no hexanucleotides were detected (see Table 2 and Fig. 2). Only the average length of mononucleotides was low, and the rest of the indicators were at a high level and accounted for the most percentage. In addition, most of the SSR loci in the chloroplast genome of S. grijsii were located in the IGS (Intergenic spacer region) region (64), and a few were located on genes (20).
Table 2
The summary of S. grijsii microsatellite types
Type | Counts | Length (bp) | Percent (%) | Average Length (bp) | Relative Abundance (loci/Mb) | Relative Density (bp/Mb) |
Mono | 60 | 661 | 71.43 | 11.02 | 378.33 | 4167.95 |
Di | 2 | 20 | 2.38 | 10 | 12.61 | 126.11 |
Tri | 8 | 96 | 9.52 | 12 | 50.44 | 605.33 |
Tetra | 13 | 160 | 15.48 | 12.31 | 81.97 | 1008.88 |
Penta | 1 | 15 | 1.19 | 15 | 6.31 | 94.58 |
Phylogenetic analysis
Cluster analysis showed that Syzygium is more closely related to Eucalyptus, Corymbia, and Angophora, followed by Plinia (see Fig. 5). Among Syzygium, S. grijsii is paraphyletic to S. jambos and is closest to S. jambos, while S. forrestii and S. cumini are sister taxa to S. malaccense. The complete chloroplast genome of S. grijsii determination has provided a new basis for elucidating the evolutionary relationships of the Myrtaceae.