Gene loss, genome rearrangement, and accelerated substitution rates in plastid genome of Hypericum ascyron (Hypericaceae)

Abstract

Background: Comparative genomic analysis exhibits dynamic evolution of plastid genome (plastome) in the clusioid clade of Malpighiales, which comprise five families, including multiple inversions and gene losses. Little is known about the plastome evolution in Hypericaceae, a large family in the clade. Only the plastome of one species, Cratoxylum cochinchinense, has been published.

Results: We generated a complete plastome sequence for Hypericum ascyron, providing the first complete plastome from the tribe Hypericeae (Hypericaceae). The H. ascyron plastome exhibits dynamic changes in gene and intron content, structure, and sequence divergence compared to the C. cochinchinense plastome from the tribe Cratoxyleae (Hypericaceae). Transcriptome data determined the evolutionary fate of the missing plastid genes infA, rps7, rps16, rpl23, and rpl32 in H. ascyron. Putative functional transfers of infA, rps7, and rpl32 were detected to the nucleus, whereas rps16 and rpl23 were substituted by nuclear-encoded homologs. The plastid rpl32 was integrated into the nuclear-encoded SODcp gene. Our findings suggested that the transferred rpl32 had undergone subfunctionalization by duplication rather than alternative splicing. The H. ascyron plastome rearrangements involved seven inversions, at least three inverted repeat (IR) boundary shifts, which generated gene relocations and duplications. Accelerated substitution rates of plastid genes were observed in the H. ascyron plastome compared with that of C. cochinchinense plastid genes. The higher substitution rates in the accD and clpP were correlated with structural change, including a large insertion of amino acids and losses of two introns, respectively. In addition, we found evidence of positive selection of the clpP, matK, and rps3 genes in the three branches related to H. ascyron. In particular, the matK gene was repeatedly under selection within the family Hypericaceae. Selective pressure in the H. ascyron matK gene was associated with the loss of trnK-UUU and relocation into the IR region.

Conclusions: The Hypericum ascyron plastome sequence provides valuable information for improving the understanding of plastome evolution among the clusioid of the Malpighiales. Evidence for intracellular gene transfer from the plastid to the nucleus was detected in the nuclear transcriptome, providing insight into the evolutionary fate of plastid genes in Hypericaceae.

Keywords: Gene substitution; Gene transfer; Inversion; Plastome; Rearrangement; matK.

Fig. 1

Map of the plastid genome of Hypericum ascyron. A Graph showing the base per base depth of the sequencing coverage across the H. ascyron plastome with one inverted repeat (IR) region. B Genes on the inside and outside of each map are transcribed in the clockwise and counterclockwise directions, respectively. The thick lines on the plastid map indicate the inverted repeats (IRA and IRB) that separate the genome into large and small single-copy regions. Ψ denotes a pseudogene. Red arrows indicate expansion events. Colored arcs on the outside of the map correspond to the locally collinear blocks inferred by Mauve (see Fig. 4)

Fig. 2

Phylogenetic distribution of gene/intron content (loss and gain) among the analyzed 10 Malpighiales

Fig. 3

Amino acid sequence of nuclear-encoded plastid-targeted genes from Hypericum ascyron. Red boxes indicate the conserved domains, and pink boxes in the N-terminus indicate a transit peptide

Fig. 4

Structural alignments of plastomes from Hypericum ascyron with three related species using Mauve. The colored blocks represent collinear sequence blocks shared by all plastomes. Blocks drawn below the horizontal line indicate sequences found in an inverted orientation. Individual genes and strandedness are represented below each genome block. Only one copy of the inverted repeat (IR) is shown for each plastome and pink boxes below each plastome block indicate its IR

Fig. 5

Variation in sequence divergence among Hypericum ascyron and Cratoxylum cochinchinense plastid protein-coding genes

Fig. 6

Plastid sequence divergence among selected Malpighiales. In the ML tree on the left, genes were selected to span the ratios of nonsynonymous to synonymous substitution rates greater than one on the branches related to Hypericum ascyron. Phylograms (right) of concatenated genes depicting nonsynonymous (d_N) and synonymous (d_S) sequence divergence for three individual genes are shown. Genes that show positive selection are selected. Red branches indicate genes with significantly higher d_N/d_S values. All trees were drawn to the same scale