The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae

Amaral, Danilo T.; Bombonato, Juliana Rodrigues; Andrade, Sónia C. S.; Moraes, Evandro M.; Franco, Fernando Faria

doi:10.1007/s00425-021-03690-5

Cited by 12 publications

(19 citation statements)

References 39 publications

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“…The significantly low values of PD recovered in areas of high endemism, such as the Sonoran and Atacama Deserts and a great part of the Caatinga and Atlantic Forests, may suggest strong lineage clustering (neoendemism), whereas the events of rapid and recent diversification of Cactaceae (Arakaki et al, 2011), such as the genus Cereus (Bombonato et al, 2020; Amaral et al, 2021), genus Pilosocereus (Bonatelli et al, 2014; Lavor et al, 2019), and Mammilloid (Breslin et al, 2021), favored the prevalence of closely related taxa. The significantly high PD in some areas, such as the Chihuahuan Desert, Peru and Ecuador Pacific coasts, the Andes, and the central portion of Dry Chaco, suggests these areas as historical refugia to the family and centers of diversification.…”

Section: Discussionmentioning

confidence: 99%

Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas

Amaral

Bonatelli

Romeiro-Brito

et al. 2022

Preprint

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Mapping biodiversity patterns across taxa and environments is crucial to address the evolutionary and ecological dimensions of species distribution, suggesting areas of particular importance for conservation purposes. Within Cactaceae, spatial diversity patterns are poorly explored, as well as the abiotic factors that may predict these patterns. We gathered geographic and genetic data from 922 cactus species, which are tightly associated with drylands, to evaluate diversity patterns, such as phylogenetic diversity and endemism, paleo-, neo-, and superendemism, and the environmental predictor variables of such patterns in a global analysis. Hotspot areas of cacti diversity are scattered along the Neotropical and Nearctic regions, mainly in the desertic portion of Mesoamerica, Caribbean Island, and the dry diagonal of South America. The geomorphological features of these regions may create a complexity of areas that work as locally buffered zones over time, which triggers local events of diversification and speciation. Desert and dryland/dry forest areas comprise paleo- and superendemism and may act as both museums and cradles of species, displaying great importance for conservation. Past climates, topography, soil features, and solar irradiance seem to be the main predictors of distinct endemism types. The hotspot areas that encompass a major part of the endemism cells are outside or poorly covered by formal protection units. The current legally protected areas are not able to conserve cactus evolutionary history. Given the rapid anthropogenic disturbance, efforts must be reinforced to monitor biodiversity and the environment and to define/plan current and new protected areas.

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Section: Discussionmentioning

confidence: 99%

Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas

Amaral

Bonatelli

Romeiro-Brito

et al. 2022

Preprint

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“…The amount of nuclear genomic data is still underexplored in the family and focused on North American cacti diversity. Currently, we recovered only three papers describing genomic sequencing and assembly [ 15 , 30 , 150 ]. From them, we found a chromosome-scale genome assembly of Hylocereus undatus , a draft of the whole genome of Carnegiae gigantea , four low-coverage genomes of species from North American cacti ( Pachycereu springlei , Lophocereus schottii , Stenocereus thurberi , and Pereskia humboldtii ), and a low-coverage genome from a South American cactus species ( Cereus fernambucensis ).…”

Section: Discussionmentioning

confidence: 99%

“…The RNA-Seq method has been used in the family for different purposes ( Table S3 ). For instance, Walker et al [ 151 ] and Wang et al [ 152 ] used this kind of dataset for phylogenomic and evolutionary studies, while other authors tested differential gene expression in cactus species under distinct ecological stress, drought event conditions, RNase-based self-incompatibility, gene expression in root development, and genes under positive selection into specific clades [ 30 , 153 , 154 , 155 , 156 , 157 , 158 ] ( Table S3 ). Thus, the application of transcriptome methodologies to study ecological and environmental stresses may provide new evidence to understand cacti adaptations [ 30 , 159 ].…”

Section: Discussionmentioning

confidence: 99%

“…Although genomics technology has advanced in the last decade, as well as the number of plant genomes available, the number of Cactaceae nuclear genomes does not follow the same pattern. Some methodological challenges might be associated with this observation, such as extraction of high-quality DNA/RNA solutions or genome assembly troubles associated with the level of ploidy, heterozygosity, and high repetitive sequence content, which seems common in Cactaceae [ 30 ]. Poor DNA/RNA quality and purity are problems commonly observed in succulent plants since they are rich in mucilage and secondary metabolites [ 162 ].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, as many species may hybridize in nature (e.g., [ 13 , 27 , 28 ]), cacti may provide many insights into hybrid zones, species cohesion, and species delimitation. Finally, due to its intrinsic association with drought stress, cacti are useful models for biogeographic approaches aiming to investigate the effects of Quaternary climate oscillations on xeric biomes (e.g., [ 21 , 29 , 30 , 31 , 32 ]). As a result, many studies with an evolutionary focus have been conducted on cacti in recent decades.…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

Franco

Amaral

Bonatelli

et al. 2022

Genes

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Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.

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A phylogeny of Cereus (Cactaceae) and the placement and description of two new species

Taylor,

Zappi,

Romeiro‐Brito

et al. 2023

TAXON

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A new study of the phylogeny of Cereus investigates generic monophyly and previous subgeneric classification. A coalescent approach was used to assess phylogenetic relationships among Cereus species based on nuclear orthologous genes captured by the Cactaceae591 probe set. The analysis included two unusual new taxa from eastern and northern Brazil to ascertain their position within the genus. Amongst the additional taxa, one was found to be early derived to the Atlantic Forest and coastal Cereus species and is described as C. ingens. Its imposing habit, considerably broader flower, yellow fruits and large seeds differentiate it from other Cereus species, and its inland agreste forest habitat in Minas Gerais and Bahia leads it to be categorized as Endangered, as little remains of this vegetation type. A second new species, C. gerardi, is described from the state of Tocantins (northern Brazil). Vegetatively this taxon is remarkable for resembling members of Pilosocereus, but has typical Cereus flowers, matching those of the type of the genus, C. hexagonus. The definition and relationships of the genus within the tribe Cereeae were made more evident, partly recovering three of the four pre‐existing subgenera.

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The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae

Cited by 12 publications

References 39 publications

Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas

Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

A phylogeny of Cereus (Cactaceae) and the placement and description of two new species

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