Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae)

Abstract

Overlapping genes occur widely in microorganisms and in some plastid genomes, but unique properties are observed when such genes span the boundaries between single-copy and repeat regions. The termini of ndhH and ndhF, situated near opposite ends of the small single-copy region (SSC) in the plastid genomes of grasses (Poaceae), have migrated repeatedly into and out of the adjacent inverted-repeat regions (IR). The two genes are transcribed in the same direction, and the 5' terminus of ndhH extends into the IR in some species, while the 3' terminus of ndhF extends into the IR in others. When both genes extend into the IR, portions of the genes overlap and are encoded by the same nucleotide positions. Fine-scale mapping of the SSC-IR junctions across a sample of 92 grasses and outgroups, integrated into a phylogenetic analysis, indicates that the earliest grasses resembled the related taxa Joinvillea (Joinvilleaceae) and Ecdeiocolea (Ecdeiocoleaceae), with ca. 180 nucleotides of ndhH extending into the IR, and with ndhF confined to the SSC. This structure is maintained in early-diverging grass lineages and in most species of the BEP clade. In the PACMAD clade, ndhH lies completely or nearly completely within the SSC, and ca. 20 nucleotides of ndhF extend into the IR. The nucleotide substitution rate has increased in the PACMAD clade in the portion of ndhH that has migrated into the SSC.

Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

“…In grasses, for example, the termini of two genes, ndhH and ndhF , were reported to have repeatedly migrated into and out of the adjacent IRs [22]. Whole rps19 was located within the LSC region in the most Gossypium cp genomes but failed to find in cp genome of G. raimondii D5 [21].…”

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

“…The junction positions between IRs and single copy regions often change among various plants due to IR contraction and expansion [36], and in Poaceae the termini of two genes, ndhH and ndhF , have migrated repeatedly into and out of the adjacent IRs [37]. Nevertheless, the junctions are nearly identical in all six cp genomes with ndhH extending 172–195 nucleotides (data not shown) into the IR, and ndhF confined to the SSC region, just like most species in the BEP clade [37].…”

Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers

“…Although each is monophyletic in molecular analyses, branching order of the BEP subfamilies has been difficult to resolve. Several recent analyses (e.g., Bouchenak-Khelladi et al, 2008;Davis and Soreng, 2010;GPWG II, 2012;Wu and Ge, 2012) support a sister relationship between Bambusoideae (B) and Pooideae (P; the bluegrasses), with the B + P clade being sister to Ehrhartoideae (E; the rices). Branching order of the three clades varies across studies, possibly as a function of outgroup sampling.…”