Correction: Understanding plastome evolution in Hemiparasitic Santalales: Complete chloroplast genomes of three species, Dendrotrophe varians, Helixanthera parasitica, and Macrosolen cochinchinensis.
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ABSTRACT:
SUBMITTER: Shin HW
PROVIDER: S-EPMC6173436 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
Correction: Understanding plastome evolution in Hemiparasitic Santalales: Complete chloroplast genomes of three species, Dendrotrophe varians, Helixanthera parasitica, and Macrosolen cochinchinensis.
Shin Hye Woo HW Lee Nam Sook NS
PloS one 20181005 10
[This corrects the article DOI: 10.1371/journal.pone.0200293.]. ...[more]
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Project description:Santalales is a large order, with over 2200 species, most of which are root or aerial (stem) hemiparasites. In this study, we report the newly assembled chloroplast genome of Dendrotrophe varians (140,666 bp) in the family Amphorogynaceae and the cp genomes of Helixanthera parasitica (124,881 bp) and Macrosolen cochinchinensis (122,986 bp), both in the family Loranthaceae. We compared the cp genomes of 11 Santalales including eight currently available cp genomes. Santalales cp genomes are slightly or not reduced in size (119-147 kb), similar to other hemiparasitic species, when compared with typical angiosperm cp genomes (120-170 kb). In a phylogeny examining gene content, the NADH dehydrogenase gene group is the only one among eight functional gene groups that lost complete functionally in all examined Santalales. This supports the idea that the functional loss of ndh genes is the initial stage in the evolution of the plastome of parasitic plants, but the loss has occurred independently multiple times in angiosperms, while they are not found in some parasites. This suggests that the functional loss of ndh genes is not essential for the transition from autotroph to parasite. We additionally examined the correlation between gene content and type of parasitism (obligate/facultative and stem/root parasites) of all hemiparasitic species in which cp genomes have been reported to date. Correlation was not found in any types of parasitism.
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Project description:Santalales is an order of plants consisting almost entirely of parasites. Some, such as Osyris, are facultative root parasites whereas others, such as Viscum, are obligate stem parasitic mistletoes. Here, we report the complete plastome sequences of one species of Osyris and three species of Viscum, and we investigate the evolutionary aspects of structural changes and changes in gene content in relation to parasitism. Compared with typical angiosperms plastomes, the four Santalales plastomes are all reduced in size (10-22% compared with Vitis), and they have experienced rearrangements, mostly but not exclusively in the border areas of the inverted repeats. Additionally, a number of protein-coding genes (matK, infA, ccsA, rpl33, and all 11 ndh genes) as well as two transfer RNA genes (trnG-UCC and trnV-UAC) have been pseudogenized or completely lost. Most of the remaining plastid genes have a significantly changed selection pattern compared with other dicots, and the relaxed selection of photosynthesis genes is noteworthy. Although gene loss obviously reduces plastome size, intergenic regions were also shortened. As plastome modifications are generally most prominent in Viscum, they are most likely correlated with the increased nutritional dependence on the host compared with Osyris.
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Project description:When a flowering plant species changes its life history from self-supply to parasite, its chloroplast genomes may have experienced functional physical reduction, and gene loss. Most species of Santalales are hemiparasitic and few studies focus on comparing the chloroplast genomes of the species from this order. In this study, we collected and compared chloroplast genomes of 12 species of Santalales and sequenced the chloroplast genomes of Taxillus nigrans and Scurrula parasitica for the first time. The chloroplast genomes for these species showed typical quadripartite structural organization. Phylogenetic analysis suggested that these 12 species of Santalales clustered into three clades: Viscum (4 spp.) and Osyris (1 sp.) in the Santalaceae and Champereia (1 sp.) in the Opiliaceae formed one clade, while Taxillus (3 spp.) and Scurrula (1 sp.) in the Loranthaceae and Schoepfia (1 sp.) in the Schoepfiaceae formed another clade. Erythropalum (1 sp.), in the Erythropalaceae, appeared as a third, most distant, clade within the Santalales. In addition, both Viscum and Taxillus are monophyletic, and Scurrula is sister to Taxillus. A comparative analysis of the chloroplast genome showed differences in genome size and the loss of genes, such as the ndh genes, infA genes, partial ribosomal genes, and tRNA genes. The 12 species were classified into six categories by the loss, order, and structure of genes in the chloroplast genome. Each of the five genera (Viscum, Osyris, Champereia, Schoepfia, and Erythropalum) represented an independent category, while the three Taxillus species and Scurrula were classified into a sixth category. Although we found that different genes were lost in various categories, most genes related to photosynthesis were retained in the 12 species. Hence, the genetic information accorded with observations that they are hemiparasitic species. Our comparative genomic analyses can provide a new case for the chloroplast genome evolution of parasitic species.
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Project description:Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.
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Project description:The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".
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Project description:Asparagus species are widely used for medicinal, horticultural, and culinary purposes. Complete chloroplast DNA (cpDNA) genomes of three Asparagus specimens collected in Hong Kong-A. aethiopicus, A. densiflorus 'Myers', and A. cochinchinensis-were de novo assembled using Illumina sequencing. Their sizes ranged from 157,069 to 157,319 bp, with a total guanine-cytosine content of 37.5%. Structurally, a large single copy (84,598-85,350 bp) and a small single copy (18,677-18,685 bp) were separated by a pair of inverted repeats (26,518-26,573 bp). In total, 136 genes were annotated for A. aethiopicus and A. densiflorus 'Myers'; these included 90 mRNA, 38 tRNA, and 8 rRNA genes. Further, 132 genes, including 87 mRNA, 37 tRNA, and 8 rRNA genes, were annotated for A. cochinchinensis. For comparative and phylogenetic analysis, we included NCBI data for four congenerics, A. setaceus, A. racemosus, A. schoberioides, and A. officinalis. The gene content, order, and genome structure were relatively conserved among the genomes studied. There were similarities in simple sequence repeats in terms of repeat type, sequence complementarity, and cpDNA partition distribution. A. densiflorus 'Myers' had distinctive long sequence repeats in terms of their quantity, type, and length-interval frequency. Divergence hotspots, with nucleotide diversity (Pi) ≥ 0.015, were identified in five genomic regions: accD-psaI, ccsA, trnS-trnG, ycf1, and ndhC-trnV. Here, we summarise the historical changes in the generic subdivision of Asparagus. Our phylogenetic analysis, which also elucidates the nomenclatural complexity of A. aethiopicus and A. densiflorus 'Myers', further supports their close phylogenetic relationship. The findings are consistent with prior generic subdivisions, except for the placement of A. racemosus, which requires further study. These de novo assembled cpDNA genomes contribute valuable genomic resources and help to elucidate Asparagus taxonomy.
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