Complete Chloroplast Genome Sequence of a Major Allogamous Forage Species, Perennial Ryegrass (Lolium perenne L.)

Diekmann, Kerstin; Hodkinson, Trevor R.; Wolfe, Kenneth H.; Bekerom, Rob Jozef Matheus van den; Dix, Philip J.; Barth, Susanne

doi:10.1093/dnares/dsp008

Cited by 67 publications

(69 citation statements)

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“…The rpoC2 gene is an exception with lower sequence identity due to various indels, as also reported in grasses [47]. One divergent hotspot region associated with a tRNA cluster in LSC ( trnS(GGA) - trnP(GAA) ) region was identified, which is inconsonant to other herb plastomes [47,48]. We also found nine highly variable noncoding regions with variation percentages above 2%.…”

Section: Discussionsupporting

confidence: 74%

“…As expected, the noncoding regions exhibited higher divergent levels than the coding regions, and the single copy regions had higher variation than the IR regions. The rpoC2 gene is an exception with lower sequence identity due to various indels, as also reported in grasses [47]. One divergent hotspot region associated with a tRNA cluster in LSC ( trnS(GGA) - trnP(GAA) ) region was identified, which is inconsonant to other herb plastomes [47,48].…”

Section: Discussionmentioning

confidence: 84%

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The Complete Chloroplast Genome Sequences of Six Rehmannia Species

Zeng

Zhou

Han

et al. 2017

Genes

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Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order. The complete genomes ranged from 153,622 bp to 154,055 bp in length, including 133 genes encoding 88 proteins, 37 tRNAs, and 8 rRNAs. Three genes (rpoA, rpoC2, accD) have potentially experienced positive selection. Plastome size variation of Rehmannia was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat (IR) region and the single-copy (SC) regions. Despite of the conserved structure in Rehmannia plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that Rehmannia was monophyletic and sister to the clade of Lindenbergia and the parasitic taxa in Orobanchaceae. The interspecific relationships within Rehmannia were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of Rehmannia.

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Section: Discussionsupporting

confidence: 74%

Section: Discussionmentioning

confidence: 84%

The Complete Chloroplast Genome Sequences of Six Rehmannia Species

Zeng

Zhou

Han

et al. 2017

Genes

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“…Comparative studies of chloroplast genomes have mostly been focused on a target species such as Panicum virgatum [22]; genera such as Oenothera [23,24]; or families such as Solanaceae [25,26], Poaceae [27,28], Pinaceae [29,30], and Asteraceae [31]. At higher taxonomic levels, information on chloroplast genomes is useful not only for phylogenetic studies [10,32,33] but also for understanding the genome evolution underlying gene and intron losses, genome size variations, and nucleotide substitutions.…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

et al. 2013

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Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.

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“…Therefore and In addition to phylogenetic analysis based on plastidic genomes, it is imperative to understand the chloroplast genome in order to logically design our next generation transplastomics. Accordingly, chloroplast genomes of many species have been sequenced (7)(8)(9)(10)(11)(12)(13)(14).…”

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confidence: 99%