The complete chloroplast genome of tall fescue (Lolium arundinaceum; Poaceae) and comparison of whole plastomes from the family Poaceae

Abstract

In this paper, we describe the complete chloroplast genome of Lolium arundinaceum. This sequence is the culmination of a long-term project completed by >400 undergraduates who took general genetics at Middle Tennessee State University from 2004-2007. It was undertaken in an attempt to introduce these students to an open-ended experiential/exploratory lesson to produce and analyze novel data. The data they produced should provide the necessary information for both phylogenetic comparisons and plastome engineering of tall fescue. The fescue plastome (GenBank FJ466687) is 136048 bp with a typical quadripartite structure and a gene order similar to other grasses; 56% of the plastome is coding region comprised of 75 protein-coding genes, 29 tRNAs, four rRNAs, and one hypothetical coding region (ycf). Comparisons of Poaceae plastomes reveal size differences between the PACC (subfamilies Panicoideae, Arundinoideae, Centothecoideae, and Chloridoideae) and BOP (subfamilies Bambusoideae, Oryzoideae, and Pooideae) clades. Alignment analysis suggests that several potentially conserved large deletions in previously identified intergenic length polymorphic regions are responsible for the majority of the size discrepancy. Phylogenetic analysis using whole plastome data suggests that fescue closely aligns with Lolium perenne. Some unique features as well as phylogenetic branch length calculations, however, suggest that a number of changes have occurred since these species diverged.

The Complete Chloroplast Genome Sequences of Six Rehmannia Species

“…As for gene contents, the same set of 88 protein-coding genes were shared by six species of Rehmannia species and highly conserved in aspect of gene number, gene function, gene order, and GC-content. Noncanonical start codons observed in this study could be also found in other angiosperms [42] and tree fern plants [43]. …”

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

“…At the IR/LSC boundaries, most IRs of non-orchid monocots contained trn H- rps 19 gene clusters, excluding Ψrpl 22 genes, leading to more-progressive expansion of IRs than that having occurred in non-monocot angiosperms [17], [20], [55], [59], [68]–[71]. In all known photosynthetic orchid cp genomes, trn H- rps 19 clusters and Ψrpl 22 genes were involved in IRs at the IR/LSC junctions.…”

“…There are 11 chloroplast-encoded ndh genes in the cp genomes of land plants, located in several transcriptional units and encoding for the thylakoid Ndh complex [72]. Non-functional chloroplast-encoded ndh genes have been found in CAM and C3 plants [32], including gymnosperms and grasses [68], [73], [74]. Sequence truncations and indels are common phenomena in orchid chloroplast-encoded ndh genes [17], [28]–[33], [75].…”

Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.)

“…The genome consists of 79,235 bp (50.48%) of protein-coding sequence, 65,831 bp (41.94%) of non-coding sequence, 2,867 bp (1.83%) of tRNA, and 9040 bp (5.76%) of rRNA. The A/T content in monocot cp genomes is well conserved (Cahoon et al, 2010) including those in the Palm family which have A/T contents of 62.8% and 62.6% in date palm and oil palm, respectively. Codon usage and codon-anticodon recognition pattern of the cp genome is described in Table 2.…”