The ndhH genes of gramminean plastomes are linked with the junctions between small single copy and inverted repeat regions

Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.

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

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.

The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation

The nuclear and plastid genomes of the plant cell form a coevolving unit which in interspecific combinations can lead to genetic incompatibility of compartments even between closely related taxa. This phenomenon has been observed for instance in Atropa-Nicotiana cybrids. We have sequenced the plastid chromosome of Atropa belladonna (deadly nightshade), a circular DNA molecule of 156,688 bp, and compared it with the corresponding published sequence of its relative Nicotiana tabacum (tobacco) to understand how divergence at the level of this genome can contribute to nuclear-plastid incompatibilities and to speciation. It appears that (1) regulatory elements, i.e., promoters as well as translational and replicational signal elements, are well conserved between the two species; (2) genes--including introns--are even more highly conserved, with differences residing predominantly in regions of low functional importance; and (3) RNA editotypes differ between the two species, which makes this process an intriguing candidate for causing rapid reproductive isolation of populations.

Ebb and flow of the chloroplast inverted repeat

The endpoints of the large inverted repeat (IR) of chloroplast DNA in flowering plants differ by small amounts between species. To quantify the extent of this movement and define a possible mechanism for IR expansion, DNA sequences across the IR-large single-copy (IR-LSC) junctions were compared among 13 Nicotiana species and other dicots. In most Nicotiana species the IR terminates just upstream of, or somewhere within, the 5' portion of the rps19 gene. The truncated copy of this gene, rps19', varies in length even between closely related species but is of constant size within a single species. In Nicotiana, six different rps19' structures were found. A phylogenetic tree of Nicotiana species based on restriction site data shows that the IR has both expanded and contracted during the evolution of this genus. Gene conversion is proposed to account for these small and apparently random IR expansions. A large IR expansion of over 12 kb has occurred in Nicotiana acuminata. The new IR-LSC junction in this species lies within intron 1 of the clpP gene. This rearrangement occurred via a double-strand DNA break and recombination between poly (A) tracts in clpP intron 1 and upstream of rps19. Nicotiana acuminata chloroplast DNA contains a "molecular fossil' of the IR-LSC junction that existed prior to this dramatic rearrangement.

The role of RNA editing in conservation of start codons in chloroplast genomes

Open reading frames (ORFs), encoded by the plastid genomes of tobacco, liverwort, rice and maize were aligned with a view to studying the conservation of translational start and stop codons created by RNA editing of homologous genes. It became evident that most of the homologous ORFs have conserved translation start and stop signals at the gene level. However, some of the ORFs show differences with respect to extensions of their 3' and 5' terminal regions. For example, the proposed N-termini of the ndhD-encoded peptides from different plant species are very variable in length and amino-acid composition. Sequence analysis of ndhD and the corresponding cDNA shows that editing of an ACG triplet in tobacco, spinach and snapdragon leads to the creation of an AUG codon, corresponding to the start codon in other species. Conservation of translational start codons of plastome-encoded genes can, therefore, be achieved by editing of transcripts, and the definition of plastome-encoded ORFs must take potential editing events into consideration.

Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16

A physical map of black pine (Pinus thunbergii) chloroplast DNA (120 kb) was constructed and two separate portions of its nucleotide sequence were determined. One portion contains trnQ-UUG, ORF510, ORF83, trnK-UUU (ORF515 in the trnK intron), ORF22, psbA, trnI-CAU (on the opposing strand) and trnH-GUG, in that order. Sequence analysis of another portion revealed the presence of a 495 bp inverted repeat containing trnI-CAU and the 3' end of psbA but lacking rRNA genes. The position of trnI-CAU is unique because most chloroplast DNAs have no gene between psbA and trnH (trnI-CAU is usually located further downstream). Black pine chloroplast DNA lacks rps16, which has been found between trnQ and trnK in angiosperm chloroplast DNAs, but possesses ORF510 instead. This ORF is highly homologous to ORF513 found in the corresponding region of liverwort chloroplast DNA and ORF563 located downstream from trnT in Chlamydomonas moewusii chloroplast DNA. A possible pathway for the evolution of black pine chloroplast DNA is discussed.