Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms

Shi, Chao; Liu, Yuan; Huang, Hui; Xia, Enhua; Zhang, Haibin; Gao, Li‐Zhi

doi:10.1371/journal.pone.0059620

Cited by 62 publications

(56 citation statements)

References 55 publications

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“…We detected no structural rearrangements, IR expansions, or gene loss-and-gain events in Camellia cp genomes. And, as the previous study [93], the ycf 15 gene, employing an ATG start codon, is likely a functional gene.…”

Section: Discussionsupporting

confidence: 52%

Comparative Chloroplast Genomes of Camellia Species

et al. 2013

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Background Camellia , comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.Methodology/Principal FindingsSeven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.Conclusions/SignificanceIn this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia . The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based “barcodes”, can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.

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Section: Discussionsupporting

confidence: 52%

Comparative Chloroplast Genomes of Camellia Species

et al. 2013

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“…Interestingly, the ycf15 gene was recently presented as a new molecular marker to effectively identify Colchicum autumnale and Gloriosa superba (Nguyen et al 2015). What is more, previous studies have suggested that ycf15 is a pseudogene and not a functional gene in angiosperms (Shi et al 2013). The ycf1 reading frame is not common in plastid genes and is usually located at the boundary of the inverted repeat (IR) and the small-single copy (SSC) regions (Raubeson and Jansen 2005).…”

Section: Features Of Plastid Genomesmentioning

confidence: 99%

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

She

Zhao

Zhou

et al. 2020

Nordic Journal of Botany

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We first report the complete chloroplast (cp) genome of Fritillaria taipaiensis and determine its characteristics, sequence divergence and phylogenetic relationships by comparing it with complete cp genomes of Liliaceae s.l. (including e.g. Nartheciaceae, Amaryllidaceae and Asparagaceae) species obtained from NCBI Genbank. We show that the ycf1, ycf15 and infA genes have become pseudogenes or are lost in some of the seventeen Liliaceae species, and that dispersed repeats are prevailing among the four types of repeats (dispersed, palindromic, complement and tandem repeats). The number of simple sequence repeats ranged from 53 to 84 in the seventeen species, with mononucleotide repeats being the most abundant, followed by dinucleotides. A total of nine genes with positive selection sites were identified (atpB, atpE, ndhF, ndhH, petB, rpl2, rpl20, rpl22 and ycf2). Furthermore, we examined 19 mutational hotspot regions, including three coding regions (rps16, infA and rpl22) and sixteen non‐coding regions. A phylogenetic analysis of the complete cp genomes and protein‐coding sequences showed that Fritillaria is most closely related to Lilium. Moreover, Asparagus and Polygonatum, Hosta and Yucca are closely related to the Liliaceae. These results will contribute to further study of evolutionary patterns and phylogenetic relationships in Liliaceae s.l.

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“…C. lineare was represented by 60 coding genes, Campynemanthe species by 5 genes, and Corsia by 5 genes in the 75-gene data matrix from the first data set. The genes infA, ycf15, and ycf68 were not included in the 75-gene data matrix because they were pseudogenes in most Liliales species examined in the present study (Shi et al 2013). The genes ycf1 and ycf2 were also excluded because high-level variations were observed in closely related taxa, which made them difficult to align.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)

Bodin

Kim

2015

Plant Mol Biol Rep

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The phylogenetic positions of the families Campynemataceae and Corsiaceae within the order Liliales remains unclear. To date, molecular data from the plastid genome of Corsiaceae has been obtained exclusively from Arachnitis, for which alignment and phylogenetic inference has proved difficult. The extent of gene conservation among mycoheterotrophic species within Corsiaceae remains unknown. To clarify the phylogenetic position of Campynemataceae and Corsiaceae within Liliales, functional plastid-coding genes of species representing both families have been analyzed. Examination of two phylogenetic data sets of plastid genes employing parsimony, maximum-likelihood, and Bayesian inference methods strongly supported both families forming a basal clade to the remaining taxa of Liliales. The first data set consists of five functional plastid-encoded genes (mat-K, rps7, rps2, rps19, and rpl2) sequenced from Corsia dispar (Corsiaceae). The data set included 31 species representing all families within Liliales, as well as selected orders that are related closely to Liliales (10 outgroup species from Asparagales, Dioscoreales, and Pandanales). The second phylogenetic analysis was based on 75 plastid genes. This data set included 18 species from Liliales, representing major clades within the order, and 10 outgroup species from Asparagales, Dioscoreales, and Pandanales. In this latter data set, Campynemataceae was represented by 60 plastid-encoded genes sequenced from herbarium material of Campynema lineare. A large proportion of the plastid genome of C. dispar was also sequenced and compared to the plastid genomes of photosynthetic plants within Liliales and mycoheterotrophic plants within Asparagales to explore plastid genome reduction. The plastid genome of C. dispar is in the advanced stages of reduction, which signifies its high dependency on mycorrhizal fungi and is suggestive of a loss in photosynthetic ability. Functional plastid genes found in C. dispar may be applicable to other species in Corsiaceae, which will provide a basis for in-depth molecular analyses of interspecies relationships within the family, once molecular data from other members become available.

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Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms

Cited by 62 publications

References 55 publications

Comparative Chloroplast Genomes of Camellia Species

Comparative Chloroplast Genomes of Camellia Species

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)

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