Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

Köhler, Matias; Reginato, Marcelo; Souza-Chies, Tatiana T.; Majure, Lucas C.

doi:10.3389/fpls.2020.00729

Cited by 46 publications

(53 citation statements)

References 163 publications

(253 reference statements)

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“…Whole genomic DNAs of all taxa were extracted using a standard CTAB protocol with silica column cleaning (see Majure et al 2019;Köhler et al 2020). DNAs were resuspended in 300 ul of TE (Tris-EDTA) buffer (pH 8.0), and DNA quantity was analyzed on a Qubit 2.0 Fluorometer.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetics of Leptocereus (Cactaceae) on Hispaniola: clarifying species limits in the L. weingartianus complex and a new species from the Sierra de Bahoruco

Majure¹,

Encarnación²,

Clase³

et al. 2021

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The Antillean genus Leptocereus represents an in-situ radiation among the Greater and Lesser Antilles of 19 currently recognized species. Extensive fieldwork carried out in the Dominican Republic over recent years has revealed that the species limits of Leptocereus of Hispaniola are more complex than previously thought. There are four currently recognized species that occur on the island, L. demissus, L. paniculatus, L. undulosus and L. weingartianus. We evaluate species limits in this group based on DNA sequence data and phylogenetic analysis, morphological characters and a survey of herbarium specimens from across Hispaniola. Based on our analyses, it is clear that at least five species occur on the island of Hispaniola, with the new species from Sierra de Bahoruco, L. velozianus, described here. We provide an identification key, distribution maps and photographic plates for all species on Hispaniola based on our own fieldwork and the study of herbarium specimens. The description of yet another species of Leptocereus on Hispaniola reiterates the importance of the poorly studied, but yet biodiverse, seasonally dry tropical forest in the Antilles.

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Section: Methodsmentioning

confidence: 99%

Phylogenetics of Leptocereus (Cactaceae) on Hispaniola: clarifying species limits in the L. weingartianus complex and a new species from the Sierra de Bahoruco

Majure¹,

Encarnación²,

Clase³

et al. 2021

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“…The best fit k-mer of 45 was selected for use in a subsequent analysis of the genomes. The quality of the newly assembled genomes was evaluated on read level basis by aligning the trimmed raw reads to the de novo assemblies using Geneious mapper, Geneious version 9.1.4 ( Kearse et al, 2012 ) with medium- to low-sensitivity option and iteration up to five times ( Köhler et al, 2020 ). Gene annotation was conducted using Plastid Genome Annotator (PGA) ( Qu et al, 2019 ) with an annotated plastome Amborella trichopoda (GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

et al. 2020

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The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

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“…All whole genomic DNAs were sent to Rapid Genomics LLC (Gainesville, FL, USA) for library preparation and sequencing using a genome skimming approach (Straub et al, 2012) on the Illumina HiSeq X Ten platform using paired‐end, 150‐bp reads. Genome skimming refers to shallow sequencing of whole‐genomic DNA, which preferentially retrieves high copy‐number portions of genomes and is thus efficient for sequencing nrDNA and plastome fractions of whole genomic DNA (see Majure et al, 2019, 2021a; Köhler et al, 2020, for the use of genome skimming in Cactaceae). Raw reads used in our plastome and ETS/ITS assemblies from all newly sequenced taxa for this study (see Appendix 1) were deposited in the NCBI Sequence Read Archive under Bioproject PRJNA650542 (https://www.ncbi.nlm.nih.gov/sra/PRJNA650542).…”

Section: Methodsmentioning

confidence: 99%

“…However, further work in other clades within Opuntioideae has revealed similar topological incongruences between plastid and ITS data (Ritz et al, 2012; L. C. Majure et al, unpublished manuscript), especially at deeper phylogenetic levels, suggesting that either paralogy or homoplasy may play a role in those poorly supported incongruences based on ITS data in Cactaceae. More recent work using plastome data has shown that Consolea was likely sister to the rest of Opuntieae (Köhler et al, 2020).…”

Section: Figurementioning

confidence: 99%

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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Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

Cited by 46 publications

References 163 publications

Phylogenetics of Leptocereus (Cactaceae) on Hispaniola: clarifying species limits in the L. weingartianus complex and a new species from the Sierra de Bahoruco

Phylogenetics of Leptocereus (Cactaceae) on Hispaniola: clarifying species limits in the L. weingartianus complex and a new species from the Sierra de Bahoruco

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

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

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