Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

Guerrero, Pablo; Majure, Lucas C.; Cornejo-Romero, Amelia; Hernández‐Hernández, Tania

doi:10.1093/jhered/esy064

Cited by 93 publications

(76 citation statements)

References 158 publications

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“…Members of Cactaceae also have experienced different alterations in their chloroplast genome. A conserved inversion of ~6 kb on the large single copy unit comprising the trnM-rbcL genes have long been suggested (Wallace 1995) and more recently confirmed (Sanderson et al 2015;Solorzano et al 2019;Majure et al 2019). Besides that, the first cactus plastome assembled from the saguaro cactus (Carnegiea gigantea (Engelm.)…”

Section: Introductionmentioning

confidence: 87%

“…All currently recognized genera in Opuntioideae (sensu Hunt et al 2006, plus Majure et al 2019 for Grusonia s.l.) were sampled with one accession per genus, resulting in a dataset of 17 taxa which were sequenced via genome-skimming (Straub et al, 2012;Majure et al 2019).…”

Section: Taxon Sampling Dna Extraction and Sequencingmentioning

confidence: 99%

“…More recently, newly assembled plastomes of seven species of the short-globose cacti of Mammillaria revealed three different plastome structures across the genus, all with two copies of a divergent inverted repeat, including (i) an extreme reduction of IRs (< 1 kb); (ii) an intermediate reduction of IR with translocation of some typical LSC genes to the IR; and (iii) a structure with a divergent IR structure and a surprisingly reduced plastome (~107 kb), being now the putative smallest plastome known for an obligately photosynthetic angiosperm (Solorzano et al 2019). Majure et al (2019), assembling chloroplast genomes for phylogenetic studies, found that ycf1 and ycf2…”

Section: Introductionmentioning

confidence: 99%

“…Likewise, the tribal classification of Opuntioideae has been controversial based on different approaches, with up to six tribes proposed (Doweld, 1999;Wallace and Dickie, 2002;Hunt 2011). Although previous studies have improved our understanding of the relationships among the major clades in Opuntioideae (Griffith & Porter 2009;Ritz et al 2012;Majure et al 2019), support for the relationships among those clades still needs to be strengthened.…”

Section: Introductionmentioning

confidence: 99%

“…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: Introductionmentioning

confidence: 87%

Section: Taxon Sampling Dna Extraction and Sequencingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

Majure

Baker

Cloud-Hughes³

et al. 2019

American J of Botany

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Premise Although numerous phylogenetic studies have been conducted in Cactaceae, whole‐plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution. Methods We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired‐end, raw reads from genome skimming were reference‐mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods. Results Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious. Conclusions This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid‐Miocene, with much of their species diversity arising in the early to mid‐Pliocene, a pattern strikingly similar to those found in other western North American desert groups.

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Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular, giantConsolea(Opuntioideae)

Majure

Barrios

Díaz³

et al. 2021

American J of Botany

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Premise The Caribbean islands are in the top five biodiversity hotspots on the planet; however, the biogeographic history of the seasonally dry tropical forest (SDTF) there is poorly studied. Consolea consists of nine species of dioecious, hummingbird‐pollinated tree cacti endemic to the West Indies, which form a conspicuous element of the SDTF. Several species are threatened by anthropogenic disturbance, disease, sea‐level rise, and invasive species and are of conservation concern. However, no comprehensive phylogeny yet exists for the clade. Methods We reconstructed the phylogeny of Consolea, sampling all species using plastomic data to determine relationships, understand the evolution of key morphological characters, and test their biogeographic history. We estimated divergence times to determine the role climate change may have played in shaping the current diversity of the clade. Results Consolea appears to have evolved very recently during the latter part of the Pleistocene on Cuba/Hispaniola likely from a South American ancestor and, from there, moved into the Bahamas, Jamaica, Puerto Rico, Florida, and the Lesser Antilles. The tree growth form is a synapomorphy of Consolea and likely aided in the establishment and diversification of the clade. Conclusions Pleistocene aridification associated with glaciation likely played a role in shaping the current diversity of Consolea, and insular gigantism may have been a key innovation leading to the success of these species to invade the often‐dense SDTF. This in‐situ Caribbean radiation provides a window into the generation of species diversity and the complexity of the SDTF community within the Antilles.

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Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

Cited by 93 publications

References 158 publications

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular, giantConsolea(Opuntioideae)

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