Chloroplast genome of <i>Tillandsia landbeckii</i> Phil. (Bromeliaceae) a species adapted to the hyper-arid conditions of the Atacama and Peruvian desert

Chávez-Galarza, Júlio; Cárdenas-Ninasivincha, Steffany; Contreras, Roberto; Ferro-Mauricio, Rubén D.; Huanca‐Mamani, Wilson

doi:10.1080/23802359.2021.1997122

Cited by 6 publications

(6 citation statements)

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“…However, two expansions of the inverted repeat (IR) at the border of the IR and the large single copy (LSC) were identified for F. bicolor and O. carnea , where the rps 3 gene of F. bicolor , and the rps 3, rpl 14, rpl 16, and partial rps 8 genes of O. carnea are translocated from the LSC to the IR relative to other Bromelioideae. Chávez-Galarza et al (2021) and Möbus et al (2021) published plastomes for Tillandsia landbeckii and for Tillandsia espinosae , Tillandsia malzinei , and Tillandsia purpurea , respectively, reporting similar structural and gene content properties to the previously published T. usneoides plastome. A recent phylogenetic study by Wu et al (2022) focusing on the order Poales, contributed four additional Bromeliaceae plastomes, belonging to the subfamilies Bromelioideae ( Cryptanthus acaulis and Neoregelia sp.)…”

Section: Introductionmentioning

confidence: 57%

“…Three potential pseudogenes were identified, including the ycf 1 and ycf 15 genes, in all studied species, and the ndh B gene only in Pseudalcantarea . The ycf 1 gene is truncated at the IRb-SSC border and has also been annotated as a pseudogene in A. comosus , T. espinosae , T. landbeckii , T. malzinei , T. purpurea , and T. usneoides ( Nashima et al, 2015 ; Poczai and Hyvönen, 2017 ; Chávez-Galarza et al, 2021 ; Möbus et al, 2021 ), as well as other monocots such as Typha latifolia (Poales), Zingiber spectabile , and Musa textilis (Zingiberales; Poczai and Hyvönen, 2017 ). The second pseudogene, ycf 15, presented premature stop codons, as found in other Bromeliaceae ( Nashima et al, 2015 ; Poczai and Hyvönen, 2017 ; Möbus et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…Full plastome sequences from the highly diverse monocot family Bromeliaceae (Poales, 3,714 spp. ; Gouda et al, 2018 ) have been published for only 13 species and one hybrid cultivar ( Nashima et al, 2015 ; Redwan et al, 2015 ; Poczai and Hyvönen, 2017 ; Paule et al, 2020 ; Chávez-Galarza et al, 2021 ; Möbus et al, 2021 ; Wu et al, 2022 ), representing three (Bromelioideae, Puyoideae, and Tillandsioideae) out of the eight Bromeliaceae subfamilies ( Givnish et al, 2007 ). In 2015, two independent research groups published the first Bromeliaceae plastomes, both from pineapple ( Ananas comosus , Bromelioideae; Nashima et al, 2015 ; Redwan et al, 2015 ), and one year later a third A. comosus plastome was published by Liu et al (2016) .…”

Section: Introductionmentioning

confidence: 99%

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New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy

et al. 2022

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Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits’ rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.

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Section: Introductionmentioning

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy

et al. 2022

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“…Next‐generation sequencing (NGS) techniques have recently been proven to be a powerful source of data to examine phylogenetic relationships at different taxonomic scales in Bromeliaceae (Machado et al, 2020; Paule et al, 2020; Chávez‐Galarza et al, 2021a, 2021b; Loiseau et al, 2021; Möbus et al, 2021, Liu et al, 2022; Vera‐Paz et al, 2022, 2023; Yardeni et al, 2022; Bratzel et al, 2023). Phylogenetic analyses based on complete plastome sequences derived from NGS have improved phylogenetic resolution and statistical support within the bromeliad subfamilies Puyoideae (Liu et al, 2022) and Tillandsioideae (Vera‐Paz et al, 2022, 2023), when compared with previous single‐ and multilocus studies based on Sanger sequenced markers.…”

Section: Introductionmentioning

confidence: 99%

“…In recent years, plastome comparative studies in Bromeliaceae have focused on describing from single (e.g., Nashima et al, 2015; Redwan et al, 2015; Poczai & Hyvönen, 2017; Chávez‐Galarza et al, 2021a, 2021b) to several species (Paule et al, 2020; Möbus et al, 2021; Liu et al, 2022; Vera‐Paz et al, 2022) representatives of the subfamilies Bromelioideae, Puyoideae, and Tillandsioideae, with 9, 13, and 37 sequenced species, respectively. A highly conserved plastome structure has generally been reported in Bromeliaceae (e.g., Redwan et al, 2015; Poczai & Hyvönen, 2017; Liu et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Expansions and contractions of the inverted repeat, as well as gene loss and potential pseudogenization shape plastome evolution in Hechtioideae (Bromeliaceae, Poales)

Ramírez‐Morillo

Espinosa-Barrera

Mendoza

et al. 2023

J of Sytematics Evolution

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Full plastomes have recently proven to be a valuable data source for resolving recalcitrant phylogenetic relationships in the flowering plant family Bromeliaceae. The study of complete plastomes has additionally led to the discovery of new structural rearrangements and advanced our understanding of bromeliad plastome diversity and evolution. Here, we focus on the study of full plastomes of the bromeliad subfamily Hechtioideae to assess phylogenetic relationships, marker informativeness, and plastome structure and evolution. Using whole‐genome sequencing data, we de novo assembled and annotated new plastid genomes of 19 Hechtioideae species plus one representative each from the Pitcairnioideae and Puyoideae subfamilies and compared them with four additional available plastomes from other bromeliad subfamilies. Our phylogenetic analysis using complete plastome sequences not only recovered the three currently recognized genera of Hechtioideae as monophyletic, strongly supporting Mesoamerantha as sister of Bakerantha and Hechtia, but also improved statistical support at different phylogenetic depths within the subfamily. We identified a set of highly informative loci, some of them explored for the first time in Hechtioideae. Structural rearrangements, including expansions and contractions of the inverted repeats, large inversions, and gene loss and potential pseudogenization were detected mainly within the genus Hechtia. Evolutionary trait rate shifts were associated with the size and guanine–cytosine content of the small single copy and inverted repeats.

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High-quality reference plastomes in Tillandsia species living at the dry limits

Kiefer,

Buchmann,

Koch

2024

Plant Syst Evol

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Ongoing climate change has had severe impacts on biota worldwide, including plants and especially those with narrow ecological niches that have adapted to extreme environments for several hundred thousand of years. Several members of the genus Tillandsia are known for their ability to live at the dry limits of life in the Atacama Desert and have potential as bioindicators for climate change at the Pacific Ocean and adjacent ecosystems. However, genomic information on these plants is scarce. In this study, five complete plastid genomes of two Tillandsia species were de novo assembled at very high quality using DNA sequence data from a combination of next-generation short-read and Sanger sequencing. The newly assembled and fully annotated plastid genomes had an average length of 156,319 base-pairs with the typical highly conserved quadripartite circular structures. Gene order and content were highly conserved, with the exception of the variable gene ycf1. The newly assembled plastid genomes were placed into a broader phylogenetic context to check the quality of sequence data obtained from past approaches relying on reference-based assemblies. It is shown that earlier presented Tillandsia plastomes are either not of sufficient quality or lack any metadata. The herein presented reference plastomes will guide future research to study parallel and convergent evolution in a reliable evolutionary framework and will allow the use of plastome data with little genetic variation for population genomics studies in species such as Tillandisa landbeckii with prevailing clonal propagation.

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Chloroplast genome of Tillandsia landbeckii Phil. (Bromeliaceae) a species adapted to the hyper-arid conditions of the Atacama and Peruvian desert

Cited by 6 publications

References 10 publications

New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy

New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy

Expansions and contractions of the inverted repeat, as well as gene loss and potential pseudogenization shape plastome evolution in Hechtioideae (Bromeliaceae, Poales)

High-quality reference plastomes in Tillandsia species living at the dry limits

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