Plastome characteristics of Cannabaceae

Abstract

Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species. To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat (IR) regions in five plastomes had experienced small expansions (330-983 bp) into the Large Single-Copy (LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes. Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell (BS = 100). Celtis, Cannabis-Humulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support (BS = 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.

Keywords: IR expansion/contraction; Phylogenomics; Plastome; Repeats; SSR; Sequence divergence.

Fig. 1

Gene maps of the plastome of Humulus scandens. Genes are indicated by boxes on the inside (clockwise transcription) and outside (counterclockwise transcription) of the outermost circle. The inner circle identifies the major structural components of the plastome (LSC, IR, and SSC). Genes belonging to different functional groups are color-coded. Dashed area in the inner circle indicates the GC content of the plastome. * represents the tRNA with an intron.

Fig. 2

Comparison of IR/SC boundaries among Cannabaceae plastomes. JSB, JSA and JLA refer to junctions of SSC/IRB, SSC/IRA, and LSC/IRA, respectively. Ψ indicates a pseudogene copy of a gene partially duplicated in the IR.

Fig. 3

The best maximum likelihood (ML) tree based on RAxML analysis. Bootstrap support values are provided next to each node.

Fig. 4

mVISTA-based identity plot showing sequence identity among Cannabaceae plastomes. Humulus scandens is set as the reference. Coding and noncoding regions are colored in blue and red, respectively.

Fig. 5

Percentages of variable (blue, top line) and parsimony-informative (red, bottom line) sites across coding and non-coding loci. A coding regions; B noncoding regions. Regions are oriented according to their genome locations.

Fig. 6

Analyses of repeated sequences in Cannabaceae plastomes. A Numbers of the three dispersed repeat types; B Numbers of tandem repeats; C Frequency of dispersed repeats by length; D Frequency of tandem repeats by length; E The locations of repeats.

Fig. 7

The distribution of the simple sequence repeats (SSRs) in Cannabaceae plastomes.