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Cactaceae Genetics and Genomics
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Cactaceae Genetics and Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2022) | Viewed by 19321

Special Issue Editors

Dr. Evandro Marsola de Moraes

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Guest Editor
Department of Biology, Federal University of São Carlos, Sorocaba, Brazil
Interests: cactaceae; population genetics; plant genetics
Dr. Fernando Faria Franco

E-Mail Website
Guest Editor
Department of Biology, Federal University of São Carlos, Sorocaba, Brazil
Interests: phylogeography; population genetics; especiation
Dr. Pablo C. Guerrero

E-Mail Website
Guest Editor
Departamento de Botánica, Facultad de Ciencias Naturales & Oceanográficas, Universidad de Concepción, Concepción, Chile
Interests: biological systematics; biogeography; conservation; biodiversity; ecology
Dr. Tania Hernández

E-Mail Website
Guest Editor
Desert Botanical Garden, Phoenix, AZ, USA
Interests: evolution; diversification of succulent lineages; phylogenetics; cactaceae evo-devo; comparative genomics

Special Issue Information

Dear Colleagues,

The succulent plants within the Cactaceae family offer an appealing model system to study the evolutionary processes driving adaptation, diversification, and persistence in arid landscapes. In the face of the accelerated desertification expansion associated with anthropogenic global warming, understanding these evolutionary processes as well as their resulting patterns offers the opportunity to improve our ability to predict the landscape’s responses to future climate changes. The cacti comprise more than 1400 species and are among the most conspicuous members of arid and semiarid landscapes in the Neotropical region. Many of these species are under extreme threat of extinction. The adaptations in the morphological, anatomical, and physiological traits acquired by members of this family in response to drought-stress selective pressure represent the most remarkable modifications observed in the plant kingdom. These evolutionary changes were then followed by intense diversification, generating an array of spectacular growth forms.

In this Special Issue, “Cactaceae Genetics and Genomics”, we aim to gather and advance the knowledge on the evolutionary genetics of cacti. We invite researchers to contribute their novel findings in the form of high-quality original research and reviews. We welcome submissions covering all aspects of the evolutionary genetics of cacti, from population-level processes to phylogenetic relationships, and using all available molecular tools, from classical molecular markers to genome and transcriptome data.

Dr. Evandro Marsola de Moraes
Dr. Fernando Faria Franco
Dr. Pablo C. Guerrero
Dr. Tania Hernández
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular markers
  • molecular phylogeny
  • phylogeography
  • phylogenomics
  • population genomics
  • transcriptomes
  • plastomes
  • genetic diversity
  • speciation
  • population genetics
  • macroevolution
  • conservation genetics
  • Cactaceae
  • molecular cytogenetics

Published Papers (6 papers)

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Research

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10 pages, 3014 KiB  
Article
Pitaya Genome and Multiomics Database (PGMD): A Comprehensive and Integrative Resource of Selenicereus undatus
by Canbin Chen, Fangping Li, Fangfang Xie, Jiaxuan Chen, Qingzhu Hua, Jianye Chen, Zhijiang Wu, Zhike Zhang, Rong Zhang, Jietang Zhao, Guibing Hu and Yonghua Qin
Genes 2022, 13(5), 745; https://doi.org/10.3390/genes13050745 - 24 Apr 2022
Cited by 17 | Viewed by 2344
Abstract
Pitaya (Selenicereus) is a kind of novel fruit with a delicious taste and superior horticulture ornamental value. The potential economic impact of the pitaya lies in its diverse uses not only as agricultural produce and processed foods but also in industrial [...] Read more.
Pitaya (Selenicereus) is a kind of novel fruit with a delicious taste and superior horticulture ornamental value. The potential economic impact of the pitaya lies in its diverse uses not only as agricultural produce and processed foods but also in industrial and medicinal products. It is also an excellent plant material for basic and applied biological research. A comprehensive database of pitaya would facilitate studies of pitaya and the other Cactaceae plant species. Here, we constructed pitaya genome and multiomics database, which is a collection of the most updated and high-quality pitaya genomic assemblies. The database contains various information such as genomic variation, gene expression, miRNA profiles, metabolite and proteomic data from various tissues and fruit developmental stages of different pitaya cultivars. In PGMD, we also uploaded videos on the flowering process and planting tutorials for practical usage of pitaya. Overall, these valuable data provided in the PGMD will significantly facilitate future studies on population genetics, molecular breeding and function research of pitaya. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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15 pages, 1332 KiB  
Article
A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae
by Monique Romeiro-Brito, Milena Cardoso Telhe, Danilo Trabuco Amaral, Fernando Faria Franco and Evandro Marsola Moraes
Genes 2022, 13(4), 707; https://doi.org/10.3390/genes13040707 - 17 Apr 2022
Cited by 6 | Viewed by 2318
Abstract
The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve [...] Read more.
The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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9 pages, 1170 KiB  
Communication
Effectiveness of Two Universal Angiosperm Probe Sets Tested In Silico for Caryophyllids Taxa with Emphasis on Cacti Species
by Delil A. Chincoya and Sofía Solórzano
Genes 2022, 13(4), 570; https://doi.org/10.3390/genes13040570 - 24 Mar 2022
Viewed by 1755
Abstract
In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of [...] Read more.
In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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14 pages, 4581 KiB  
Article
A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae
by Serena Acha and Lucas C. Majure
Genes 2022, 13(2), 350; https://doi.org/10.3390/genes13020350 - 15 Feb 2022
Cited by 12 | Viewed by 2645
Abstract
Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need [...] Read more.
Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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13 pages, 1333 KiB  
Article
Independent Evolutionary Lineages in a Globular Cactus Species Complex Reveals Hidden Diversity in a Central Chile Biodiversity Hotspot
by Heidy M. Villalobos-Barrantes, Beatriz M. Meriño, Helmut E. Walter and Pablo C. Guerrero
Genes 2022, 13(2), 240; https://doi.org/10.3390/genes13020240 - 27 Jan 2022
Cited by 3 | Viewed by 3654
Abstract
Unraveling the processes involved in the origin of a substantial fraction of biodiversity can be a particularly difficult task in groups of similar, and often convergent, morphologies. The genus Eriosyce (Cactaceae) might present a greater specific diversity since much of its species richness [...] Read more.
Unraveling the processes involved in the origin of a substantial fraction of biodiversity can be a particularly difficult task in groups of similar, and often convergent, morphologies. The genus Eriosyce (Cactaceae) might present a greater specific diversity since much of its species richness might be hidden in morphological species complexes. The aim of this study was to investigate species delimitation using the molecular data of the globose cacti “E. curvispina”, which harbor several populations of unclear evolutionary relationships. We ran phylogenetic inferences on 87 taxa of Eriosyce, including nine E. curvispina populations, and by analyzing three plastid noncoding introns, one plastid and one nuclear gene. Additionally, we developed 12 new pairs of nuclear microsatellites to evaluate the population-level genetic structure. We identified four groups that originated in independent cladogenetic events occurring at different temporal depths; these groups presented high genetic diversity, and their populations were genetically structured. These results suggest a complex evolutionary history in the origin of globular cacti, with independent speciation events occurring at different time spans. This cryptic richness is underestimated in the Mediterranean flora of central Chile, and thus unique evolutionary diversity could be overlooked in conservation and management actions. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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Review

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22 pages, 2366 KiB  
Review
Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects
by Fernando Faria Franco, Danilo Trabuco Amaral, Isabel A. S. Bonatelli, Monique Romeiro-Brito, Milena Cardoso Telhe and Evandro Marsola Moraes
Genes 2022, 13(3), 452; https://doi.org/10.3390/genes13030452 - 01 Mar 2022
Cited by 7 | Viewed by 4272
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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