Horizontal gene transfer from flowering plants to Gnetum

Abstract

Although horizontal gene transfer is well documented in microbial genomes, no case has been reported in higher plants. We discovered horizontal transfer of the mitochondrial nad1 intron 2 and adjacent exons b and c from an asterid to Gnetum (Gnetales, gymnosperms). Gnetum has two copies of intron 2, a group II intron, that differ in their exons, nucleotide composition, domain lengths, and structural characteristics. One of the copies, limited to an Asian clade of Gnetum, is almost identical to the homologous locus in angiosperms, and partial sequences of its exons b and c show characteristic substitutions unique to angiosperms. Analyses of 70 seed plant nad1 exons b and c and intron 2 sequences, including representatives of all angiosperm clades, support that this copy originated from a euasterid and was horizontally transferred to Gnetum. Molecular clock dating, using calibrations provided by gnetalean macrofossils, suggests an age of 5 to 2 million years for the Asian clade that received the horizontal transfer.

Fig. 1.

Relative location of the five nad1 exons in the Petunia mt genome and a predicted secondary structure of the gymnosperm-type mt nad1 intron 2 of Gnetum gnemonoides.(A) Arrows indicate the 5′ → 3′ orientation of the nad1 exon regions. An asterisk in the intron 2 scheme indicates the intervening nucleotides of the Gnetum gymnosperm-type intron. Mitochondrial map modified from Conklin et al. (6). (B) Domain lengths before the slash refer to Gnetum gymnosperm-type introns, those after the slash to Gnetum angiosperm-type introns.

Fig. 2.

Alignment of mt nad1 exons b and c. Dots indicate identity to topmost sequence; dashes indicate gaps; question marks indicate missing data. Numbers in brackets indicate lengths of intron; N/A and an asterisk after the intron length indicate incomplete intron sequences; dashes indicate lack of intron. Amino acid translation is given for Gnetum gymnosperm-type exon sequences, and amino acids that have undergone RNA editing (–7) are given in parentheses. Dots above the topmost sequence indicate the posttranscriptionally edited sites. The specific Gnetum gymnosperm-type and angiosperm-type introns included are those of G. klossii. The Gnetum angiosperm-type nad1 exon b is characterized by a 4-nt (GATA) insertion. IBS1 indicates the intron binding site. See Table 2 for GenBank accession numbers.

Fig. 3.

Distribution of mt nad1 partial exons b and c and intron 2, and age estimates for Gnetum crown groups. (A) Bootstrap majority-rule consensus tree obtained from conserved intron and exon sections analyzed by neighbor-joining, using GTR + G + I distances (α = 0.097 and P_inv = 0.120). (B) Distribution of the gymnosperm- and angiosperm-type introns on the maximum likelihood tree obtained from concatenated Gnetum nuclear and plastid sequences. Filled squares indicate intron presence; hatched squares represent partially sequenced or PCR-verified accessions; open squares indicate lack of intron. No introns were detected in G. africanum and Welwitschia. Numbers next to nodes represent parsimony bootstrap support, followed by Bayesian posterior probabilities. (C) Age estimates for Gnetum crown groups from chloroplast matK and rbcL sequences. Arrows indicate nodes constrained by fossils. a, age of Gnetales (205–125 my, depending on the fossil used); b, age of the Gnetum-Welwitschia divergence (115–70 my); c, age of extant Gnetum (11–6 my); d, age of Asian Gnetum; e, age of Asian clade II Gnetum.