Plastid phylogenomic insights into the evolution of Caryophyllales

Yao, Gang; Jin, Jianjun; Li, Hongtao; Yang, Jun‐Bo; Mandala, Venkata S.; Croley, Matthew; Mostow, Rebecca S.; Douglas, Norman A.; Chase, Mark W.; Christenhusz, Maarten J. M.; Soltis, Douglas E.; Soltis, Pamela S.; Smith, Stephen A.; Brockington, Samuel F.; Moore, Michael J.; Yi, Ting‐Shuang; D, Li

doi:10.1016/j.ympev.2018.12.023

Cited by 125 publications

(163 citation statements)

References 117 publications

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“…A model to explain the major rearrangements observed in the Lamprocapnos spectabilis The Opuntia quimilo plastome reinforces some different putative structural synapomorphies that have been reported in Caryophyllales. For example, the loss of the rpl2 intron, previously suggested to be absent throughout the Centrospermae (Palmer et al 1988), is supported in our study and others newly assembled plastomes in Caryophyllales (Yao et al 2019 likely experienced independent losses of several genes of the ndh suite in their chloroplast genomes, although this was not so for tribe Opuntieae, where those genes were found to be intact ( Fig. 5, red stars).…”

Section: Insights From Chloroplast Genome Assemblies In Opuntioideae supporting

confidence: 85%

“…In this case, nextgeneration sequencing (NGS) could be a useful tool, since it has transformed the study of nonmodel plant taxa in phylogenetic inferences with high throughput data allowing deep resolutions across major plant clades (Xi et al 2012;Ma et al 2014;Gardner et al 2016;Zong et al 2019). NGS data are also showing to be extremely useful for discovering informative regions across genomes, for marker development (Wu et al 2010;Dong et al 2012;Ripma et al 2014;Reginato et al 2016), as well as to investigate chloroplast genome evolution (Dong et al 2013;Mower & Vickrey 2018;Yao et al 2019). Nevertheless, this approach is still in its infancy across Cactaceae (Majure et al 2019) and remains a path to be explored.…”

Section: Introductionmentioning

confidence: 99%

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Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (~25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

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Section: Insights From Chloroplast Genome Assemblies In Opuntioideae supporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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“…Seven species from Achatocarpaceae, Aizoaceae and Amaranthaceae s.l. were selected as outgroups, based on phylogenetic relationships constructed recently (Yao et al 2019). Phylogenetic result showed that all of the Caryophyllaceae members formed a well-supported clade and P. tunicoides clustered within the tribe Caryophylleae with 100% bootstrap support value (Figure 1), in agreement with previously published phylogenetic study (Greenberg and Donoghue 2011).…”

supporting

confidence: 84%

Characterization of the complete plastid genome of Psammosilene tunicoides (Caryophyllaceae), an endangered medical herb endemic to south-western China

Huang

Yao

2019

Mitochondrial DNA Part B

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Psammosilene tunicoides is an endangered medical herb endemic to south-western China. In this study, the complete plastid genome of the species was characterized and assembled using the next-generation DNA sequencing method. The plastid genome is 153,978 bp in length, including a large single copy (LSC) region of 83,981 bp and a small single copy (SSC) region of 17,489 bp, which were separated by a pair of inverted repeat (IR) regions of 26,254 bp. The genome encoded 112 unique genes, including 78 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content of the whole genome is 36.49%. The phylogenetic analysis based on 17 plastid genome of Caryophyllaceae revealed that P. tunicoides nested within the tribe Caryophylleae with strong support value. ARTICLE HISTORY

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“…This technique is an optimized version of ddRADseq (double digest restriction‐site associated DNA sequencing) specifically intended for large‐scale genotyping experiments (https://www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/slaf-seq.html?langsel=/us/) using deep sequencing to ensure genotyping accuracy and predesigning reduced representation library (RRL) schemes to avoid large numbers of repetitive sequences (Sun et al., 2013; Wang et al., 2019). After a pilot study, two restriction enzymes ( Mse I and Hae III) were selected based on the uniqueness and uniformity of the obtained fragments, which were aligned to the reference genome of Tartary buckwheat (Zhang et al., 2017), which diverged from Rheum ~62 Ma (Yao et al., 2019). Methodological details for SLAF‐seq are described in detail in Sun et al.…”

Section: Methodsmentioning

confidence: 99%

Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region

et al. 2020

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Allopatric divergence is often initiated by geological uplift and restriction to sky‐islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographical structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants, we used population genomic data of the Rheum palmatum complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection, to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the R. palmatum complex originated in the central Hengduan Mts and possibly in regions further east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the R. palmatum complex cannot reject a restriction to sky‐islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographical areas.

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Plastid phylogenomic insights into the evolution of Caryophyllales

Cited by 125 publications

References 117 publications

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Characterization of the complete plastid genome of Psammosilene tunicoides (Caryophyllaceae), an endangered medical herb endemic to south-western China

Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region

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