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Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far.

Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes.

Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny.

Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.

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.Consoleaconsists 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.

We reconstructed the phylogeny ofConsolea, 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.

Consoleaappears 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 ofConsoleaand likely aided in the establishment and diversification of the clade.

Pleistocene aridification associated with glaciation likely played a role in shaping the current diversity ofConsolea, 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.

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.

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.

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 inCylindropuntia(e.g., spiny fruit) are mostly homoplasious.

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.

In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics.

Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information.

The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence ofrps16andrpl2pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%.

Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.