Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Int J Mol Sci
2018 Nov 28;1912:. doi: 10.3390/ijms19123780.
Show Gene links
Show Anatomy links
Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics.
He D
,
Gichira AW
,
Li Z
,
Nzei JM
,
Guo Y
,
Wang Q
,
Chen J
.
???displayArticle.abstract???
The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.
XDB31010000 the Strategic Priority Research Program of Chinese Academy of Sciences, 31570220 the National Natural Science Foundation of China, Y655261W03 Wuhan Botanical Garden, Chinese Academy of Sciences
Figure 1. Circular gene maps of five chloroplast genomes of Nymphaeaceae. Grey arrows indicate the direction in which genes are transcribed. Color codes indicates the various gene functional groups, and the grey-shaded part in the inner circle shows the GC level of each chloroplast genome.
Figure 2. Details of codon preferences (bar) and relative synonymous codon usage values (line) of 12 chloroplast genomes of Nymphaeaceae.
Figure 3. Number of RNA-editing sites in each of the transcripts of 19 common genes in all analyzed chloroplast genomes.
Figure 4. Comparison of the border positions of the large single copy, small single copy, and the inverted-repeat regions among chloroplast genomes of twelve species of Nymphaeaceae. Complete genes and portions of genes adjacent to the junctions are depicted by differently colored blocks.
Figure 5. Mauve software alignment of the whole chloroplast genome of 12 species of Nymphaeaceae. Local collinear blocks representing identical gene clusters are depicted by the same color and are connected by lines.
Figure 6. Phylogenetic relationships among the species of Nymphaeaceae, Cabombaceae, and Hydatellaceae (outgroup). The Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic tree was based on 66 protein codon genes. The numbers indicate ML bootstrap support (100) and BI posterior probabilities (1.0) values. The - symbol indicates maximum support. The first two values and the last two are for unpartitioned data and partitioned data respectively.
Beier,
MISA-web: a web server for microsatellite prediction.
2017, Pubmed
Beier,
MISA-web: a web server for microsatellite prediction.
2017,
Pubmed
Biswal,
Phylogenetic reconstruction in the order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding.
2012,
Pubmed
,
Echinobase
Chumley,
The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.
2006,
Pubmed
Clegg,
Rates and patterns of chloroplast DNA evolution.
1994,
Pubmed
Daniell,
Chloroplast genomes: diversity, evolution, and applications in genetic engineering.
2016,
Pubmed
Darling,
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
2004,
Pubmed
Darriba,
jModelTest 2: more models, new heuristics and parallel computing.
2012,
Pubmed
De Las Rivas,
Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.
2002,
Pubmed
Delsuc,
Phylogenomics and the reconstruction of the tree of life.
2005,
Pubmed
Edgar,
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
2004,
Pubmed
Freyer,
Occurrence of plastid RNA editing in all major lineages of land plants.
1997,
Pubmed
Friedman,
Hydatellaceae are water lilies with gymnospermous tendencies.
2008,
Pubmed
Gandhi,
Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family.
2010,
Pubmed
Gitzendanner,
Plastid phylogenomic analysis of green plants: A billion years of evolutionary history.
2018,
Pubmed
Goremykin,
The evolutionary root of flowering plants.
2013,
Pubmed
Goremykin,
Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm.
2003,
Pubmed
Graham,
Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots.
2002,
Pubmed
Gruenstaeudl,
Bioinformatic Workflows for Generating Complete Plastid Genome Sequences-An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade.
2018,
Pubmed
Jansen,
Methods for obtaining and analyzing whole chloroplast genome sequences.
2005,
Pubmed
Jansen,
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.
2007,
Pubmed
Jian,
Resolving an ancient, rapid radiation in Saxifragales.
2008,
Pubmed
Kumar,
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
2016,
Pubmed
Kurtz,
REPuter: the manifold applications of repeat analysis on a genomic scale.
2001,
Pubmed
Lanfear,
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.
2017,
Pubmed
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Leebens-Mack,
Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.
2005,
Pubmed
Les,
Molecular evolutionary history of ancient aquatic angiosperms.
1991,
Pubmed
Li,
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review.
2002,
Pubmed
Liu,
Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation.
2010,
Pubmed
Liu,
Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.
2005,
Pubmed
Lohse,
OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes.
2007,
Pubmed
Luo,
Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales.
2016,
Pubmed
Moore,
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms.
2007,
Pubmed
Moore,
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots.
2010,
Pubmed
Mower,
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments.
2009,
Pubmed
Padgett,
Phylogenetic relationships in Nuphar (Nymphaeaceae): evidence from morphology, chloroplast DNA, and nuclear ribosomal DNA.
1999,
Pubmed
Parkinson,
Multigene analyses identify the three earliest lineages of extant flowering plants.
2000,
Pubmed
Raubeson,
Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus.
2007,
Pubmed
Ronquist,
MrBayes 3: Bayesian phylogenetic inference under mixed models.
2003,
Pubmed
Saarela,
Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree.
2007,
Pubmed
Sharp,
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
1987,
Pubmed
Soltis,
Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology.
1999,
Pubmed
Stamatakis,
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
2014,
Pubmed
Stefanović,
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
2004,
Pubmed
Sun,
Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.
2016,
Pubmed
Tillich,
GeSeq - versatile and accurate annotation of organelle genomes.
2017,
Pubmed
Wang,
Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots.
2008,
Pubmed
Wheeler,
NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS.
1990,
Pubmed
Wu,
Amino acids: metabolism, functions, and nutrition.
2009,
Pubmed
Wyman,
Automatic annotation of organellar genomes with DOGMA.
2004,
Pubmed
Xiao-Ming,
Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants.
2017,
Pubmed
Zerbino,
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
2008,
Pubmed