Shifeng Cheng’s scientific contributions

Percentage of reads in each edited site from total reads in the mitogenome. Coverage goes from 102 times up to 44015 times (in position 63551, nad5 gene). (PDF)

RNA edited sites in the mitogenome of L. dussii. (DOCX)

Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plastome (155,956 bp) and mitogenome (212,153 bp) of the hornwort Leiosporoceros dussii, the sister taxon to all hornworts. The Leiosporoceros organellar genomes show conserved gene structure and order with respect to the other hornworts and other bryophytes. Additionally, using RNA-seq data we quantified the frequency of RNA-editing events (the canonical C-to-U and the reverse editing U-to-C) in both organellar genomes. In total, 109 sites were found in the plastome and 108 in the mitogenome, respectively. The proportion of edited sites corresponds to 0.06% of the plastome and 0.05% of the mitogenome (in reference to the total genome size), in contrast to 0.58% of edited sites in the plastome of Anthoceros angustus (161,162 bp). All edited sites in the plastome and 88 of 108 sites in the mitogenome are C-to-U conversions. Twenty reverse edited sites (U-to-C conversions) were found in the mitogenome (17.8%) and none in the plastome. The low frequency of RNA editing in Leiosporoceros, which is nearly 88% less than in the plastome of Anthoceros and the mitogenome of Nothoceros, indicates that the frequency of RNA editing has fluctuated during hornwort diversification. Hornworts are a pivotal land plant group to unravel the genomic implications of RNA editing and its maintenance despite the evident evolutionary disadvantages.

A. Transcriptome read coverage of the L. dussii plastome. The x-axis shows the gene map of this genome, starting with the LSC region, while the y-axis indicates read depth. B. Transcriptome read coverage of the L. dussii mitogenome. The x-axis shows the gene map of this genome, while the y-axis indicates read depth. A color-coded scale classifies the genes into functional categories. (EPS)

Number of RNA edited sites per gene in the Leiosporoceros and Anthoceros plastomes. The numbers on the right of the histograms indicate the edited sites that are shared between the two hornworts. (TIFF)

Percentage of reads in each edited site with respect to total reads in the plastome. Coverage goes from 165 times up to 65770 times (in position 85532, PsaM). (PDF)

RNA edited sites in the plastome of L. dussii. (DOCX)