Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

Abstract

BackgroundCymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution.ResultsThe complete nucleotide sequences of eight individuals from a total of five Cymbidium species’ chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae.ConclusionsPhylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification—organelle-scale “barcodes”, and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.

The Complete Plastid Genome Sequence of Iris gatesii (Section Oncocyclus), a Bearded Species from Southeastern Turkey

“…Studies by Guisinger et al (2010) showed that while Poaceae genera either lack accD, ycf1, and ycf 2 genes entirely or have lost all except remnants of these genes, Typha latifolia (Typhaceae, Poales) retains them. Yang et al (2013) sequenced five Cymbidium Sw. species and found that unlike Phalaenopsis the Cymbidium species retained most of their ndh genes although only a few of these retained genes were functional. Studies on the palm family (Arecaceae, Arecales) have revealed a plastid genome that is typical for angiosperms, although ycf1 was determined to be a pseudogene in the family .…”

“…Orchidaceae are early diverging within Asparagales (Pires et al 2006;Seberg et al 2012;Chen et al 2013) and are estimated to have a stem node age of 95.7 MYA and a crown node age of 51.6 MYA (Chen et al 2013). The orchid plastid genomes investigated to date lack all or some of their ndh genes or coding functions (Chang et al 2006;Wu et al 2010;Pan et al 2012;Yang et al 2013) and are unlikely to be typical for other members of Asparagales such as Iridaceae.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…The SC/IR boundaries showed only slight differences, for example, at ycf1 and ѱycf1 (Figure 4). This phenomenon is relatively common in other cp genomes [8,16,21]. Several genes, including ndhF, rps19, and trnH, had almost identical locations and sizes among Fritillaria.…”

“…The cp genome ranges from 120 to 180 kb in higher plants and has a quadripartite structure consisting of a large single copy (LSC) and small single copy (SSC) region and two copies of a larger inverted repeat (IR) [7]. The cp genome encodes 110 to 130 genes with up to 80 unique protein-coding genes, four ribosomal RNAs (rRNAs), and approximately 30 transfer RNAs (tRNAs) [8,9]. However, a few parasitic plants have small chloroplast genomes due to unique life cycles [10].…”

Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research

“…Many studies have indicated that chloroplast DNA contains a great deal of genetic variation between species and populations (Wojciechowski et al, 2004;Byrne and Hankinson, 2012;Yang et al, 2013). Non-coding areas of SC regions are frequently used in phylogenetic analysis of lower plants (Clegg et al, 1994).…”