Aroideae is the largest and most diverse subfamily of the plant family Araceae. Despite its agricultural and horticultural importance, the genomic resources are sparse for this subfamily. Here, we ...report de novo assembled and fully annotated chloroplast genomes of 13 Aroideae species. The quadripartite chloroplast genomes (size range of 158,177–170,037 bp) are comprised of a large single copy (LSC; 75,594–94,702 bp), a small single copy (SSC; 12,903–23,981 bp) and a pair of inverted repeats (IRs; 25,266–34,840 bp). Notable gene rearrangements and IRs contraction / expansions were found for Anchomanes hookeri and Zantedeschia aethiopica. Codon usage, amino acid frequencies, oligonucleotide repeats, GC contents, and gene features revealed similarities among the 13 species. The number of oligonucleotide repeats was uncorrelated with genome size or phylogenetic position of the species. Phylogenetic analyses corroborated the monophyly of Aroideae but were unable to resolve the positions of Calla and Schismatoglottis.
•Genomic resources are sparse for subfamily Aroideae, Araceae.•Chloroplast genomes of thirteen species of subfamily Aroideae were de novo assembled.•Comparative analyses of chloroplast genomes were performed among these species.•Unique Inverted Repeats contraction and expansion and unique rearrangement of genes in species of subfamily Aroideae.
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•Crassulacean acid metabolism (CAM) arose three independent times in the Agavoideae.•C3 ancestors of CAM species show anatomical similarities to CAM species.•Evolution of CAM in the ...Agavoideae was predated by the origin of CAM leaf traits.
Crassulacean acid metabolism (CAM) is a modified form of photosynthesis that has arisen independently at least 35 times in flowering plants. The occurrence of CAM is often correlated with shifts to arid, semiarid, or epiphytic habits, as well as transitions in leaf morphology (e.g. increased leaf thickness) and anatomy (e.g. increased cell size and packing). We assess shifts between C3 and CAM photosynthesis in the subfamily Agavoideae (Asparagaceae) through phylogenetic analysis of targeted loci captured from the nuclear and chloroplast genomes of over 60 species. Carbon isotope data was used as a proxy for mode of photosynthesis in extant species and ancestral states were estimated on the phylogeny. Ancestral character state mapping suggests three independent origins of CAM in the Agavoideae. CAM species differ from C3 species in climate space and are found to have thicker leaves with densely packed cells. C3 ancestors of CAM species show a predisposition toward CAM-like morphology. Leaf characteristics in the ancestral C3 species may have enabled the repeated evolution of CAM in the Agavoideae subfamily. Anatomical changes, including a tendency toward 3D venation, may have initially arisen in C3 ancestors in response to aridity as a way to increase leaf succulence for water storage.
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed ...subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are reduced in regions near genes and within TEs in the first-generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. Subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events and may also contribute to uncovering the mechanistic basis of heterosis and subgenome dominance.
Main conclusion
This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust ...molecular markers for phylogenetic inference.
Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species:
Spathiphyllum patulinervum
,
Stenospermation multiovulatum
,
Monstera adansonii
, and
Rhaphidophora amplissima
. The quadripartite chloroplast genomes (size range 163,335–164,751 bp) consist of a pair of inverted repeats (25,270–25,931 bp), separating a small single copy region (21,448–22,346 bp) from a large single copy region (89,714–91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including
psbK
,
ndhK
,
ndhD
,
rbcL
,
accD
,
rps8
, and
ycf2
. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus
Spathiphyllum
and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.
Unresolved questions about evolution of the large and diverse legume family include the timing of polyploidy (whole-genome duplication; WGDs) relative to the origin of the major lineages within the ...Fabaceae and to the origin of symbiotic nitrogen fixation. Previous work has established that a WGD affects most lineages in the Papilionoideae and occurred sometime after the divergence of the papilionoid and mimosoid clades, but the exact timing has been unknown. The history of WGD has also not been established for legume lineages outside the Papilionoideae. We investigated the presence and timing of WGDs in the legumes by querying thousands of phylogenetic trees constructed from transcriptome and genome data from 20 diverse legumes and 17 outgroup species. The timing of duplications in the gene trees indicates that the papilionoid WGD occurred in the common ancestor of all papilionoids. The earliest diverging lineages of the Papilionoideae include both nodulating taxa, such as the genistoids (e.g., lupin), dalbergioids (e.g., peanut), phaseoloids (e.g., beans), and galegoids (=Hologalegina, e.g., clovers), and clades with nonnodulating taxa including Xanthocercis and Cladrastis (evaluated in this study). We also found evidence for several independent WGDs near the base of other major legume lineages, including the Mimosoideae-Cassiinae-Caesalpinieae (MCC), Detarieae, and Cercideae clades. Nodulation is found in the MCC and papilionoid clades, both of which experienced ancestral WGDs. However, there are numerous nonnodulating lineages in both clades, making it unclear whether the phylogenetic distribution of nodulation is due to independent gains or a single origin followed by multiple losses.
Practical considerations for plant phylogenomics McKain, Michael R.; Johnson, Matthew G.; Uribe‐Convers, Simon ...
Applications in plant sciences,
March 2018, Letnik:
6, Številka:
3
Journal Article
Recenzirano
Odprti dostop
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read ...technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project‐dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up‐and‐coming technologies that may help propel the field even further.
Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ...ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.
The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, ...Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C ₄ species with a high frequency of polyploids. A phylogeny was constructed for ca . 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C ₄ grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum . We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation.
Significance Duplication of genomes following hybridization (allopolyploidy) is common among flowering plants, particularly in the grasses that cover vast areas of the world and provide food and fuel. Here, we find that genome duplication has occurred at a remarkable rate, accounting for at least a third of all speciation events in a group of about 1,200 species. Much of this genome duplication occurred during the expansion of the C ₄ grasslands in the Late Miocene. We find no evidence that allopolyploidy leads directly to a change in the net rate of diversification or correlates with the origin of novel morphological characters. However, as a mode of speciation, the frequency of allopolyploidization is surprisingly high.
•Many recent and ancient allopolyploids exhibit subgenome dominance.•Extensive homoeologous exchanges complicate accurate subgenome assignments.•Allopolyploid history may be obscured by biased ...homoeologous exchanges.•Subgenome assignment should, if possible, incorporate phylogenetic approaches.
Whole genome duplications (WGDs), also known as polyploid events, have played a crucial role in the evolutionary success of angiosperms across recent and ancient timescales. A recurrent observation from the analysis of allopolyploids is that one of the parental subgenomes is generally more dominant, referred to as ‘subgenome dominance’, based on higher gene content and expression patterns. Subgenome dominance has far reaching implications to research areas ranging from crop improvement efforts to evolutionary and ecological studies. However, the analysis of subgenome dominance in more ancient polyploids is complicated by a long history of homoeologous exchanges among subgenomes. Here, we will discuss how resulting homoeolog rearrangements and replacements have been ignored in previous studies and urge future studies to integrate phylogenetic approaches to assign homoeologs to parental subgenomes.
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