The complete pineapple (<i>Ananas comosus</i>; Bromeliaceae) varieties F153 chloroplast genome sequence

Liu, Jin; Niu, Ying-Feng; Liu, Shihong; Ni, Shu-Bang

doi:10.1080/23802359.2016.1174084

Cited by 6 publications

(5 citation statements)

References 4 publications

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“…bicolor-MN563795), and only one represents the genus Tillandsia. Only the plastomes of Ananas (Nashima et al 2015;Redwan et al 2015) and Tillandsia usneoides (Poczai and Hyvönen 2017) have been discussed in detail, the other GenBank submissions remained largely unexplored in earlier studies (Liu et al 2016;Paule et al 2020a, b).…”

Section: Bromeliaceae High-quality Reference Genomesmentioning

confidence: 99%

Setting the evolutionary timeline: Tillandsia landbeckii in the Chilean Atacama Desert

et al. 2021

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The Chilean Atacama Desert is among the oldest deserts of the world. Here, Tillandsia landbeckii is forming a unique vegetation type known as Tillandsia lomas. This vegetation consists in its typical configuration of one single vascular plant species only and forms regular linear structures in a sloped landscape and is largely depending on fog occurrence as dominant source of water supply. Without developing a typical root system, there are only few other terrestrial Tillandsia species growing on bare sand in Chile and Peru such as T. marconae, T. virescens, T. purpureaor T. latifolia. Although phylogenetic evidence is limited, convergent evolution of this unique growth behavior is evident. The predominantly arid and hyper-arid climate exists since the Early Miocene, which raises the question about timing of T. landbeckii evolutionary history. Phylogenomic analyses using whole plastome sequence data highlight the onset of diversification in T. landbeckii approximately 500,000 years ago. We also demonstrate subsequent secondary genetic contact with T. purpurea during the Late Pleistocene using DNA sequence data and genome size estimates, which resulted into the formation of T. marconae.

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Section: Bromeliaceae High-quality Reference Genomesmentioning

confidence: 99%

Setting the evolutionary timeline: Tillandsia landbeckii in the Chilean Atacama Desert

et al. 2021

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“…; 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) . Poczai and Hyvönen (2017) published the Spanish moss ( Tillandsia usneoides , Tillandsioideae) plastome, reporting a highly conserved structure, gene content and gene order relative to the plastome of the distantly related A. comosus .…”

Section: Introductionmentioning

confidence: 99%

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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“…Voucher specimens (LNH180701015) were deposited in the Herbarium of Lingnan Normal University, Zhanjiang, China. The experiment procedure was as reported in Liu et al (2016). Total DNA of the L. congestiflora was sequenced with secondgeneration sequencing technology (Illumina HiSeq 2000, San Diego, CA).…”

mentioning

confidence: 99%

“…The experiment procedure was as reported in Liu et al. ( 2016 ). Total DNA of the L. congestiflora was sequenced with second-generation sequencing technology (Illumina HiSeq 2000, San Diego, CA).…”

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confidence: 99%

Complete plastome sequence of Lysimachia congestiflora Hemsl. a medicinal and ornamental species in Southern China

Cheng

Chen

et al. 2019

Mitochondrial DNA Part B

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Lysimachia congestiflora Hemsl. is a perennial herb of Primulaceae. It is mainly distributed in the provinces to the south of the Changjiang River and south of Shanxi, Gansu province and Taiwan. It is a plant that combines medicinal, ornamental, and economic values. To date no study has been carried out on the genome of L. congestiflora. Here, we report and characterize the complete plastid genome sequence of L. congestiflora in order to provide genomic resources useful for promoting its conservation. The complete chloroplast genome of L. congestiflora is 154,505 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 84,606 bp), a single-copy region (SSC, 17,961 bp), and a pair of inverted repeats (IRs, 25,969 bp). There are 114 annotated genes, including 80 unique protein-coding genes, 4 unique ribosomal RNA genes, and 30 transfer RNA genes. To investigate the evolution status of L. congestiflora, as well as Primulaceae, we constructed a phylogenetic tree with L. congestiflora and other 11 species based on their complete chloroplast genomes. According to the phylogenetic topologies, L. congestiflora was closely related to L. coreana.

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The complete pineapple (Ananas comosus; Bromeliaceae) varieties F153 chloroplast genome sequence

Cited by 6 publications

References 4 publications

Setting the evolutionary timeline: Tillandsia landbeckii in the Chilean Atacama Desert

Setting the evolutionary timeline: Tillandsia landbeckii in the Chilean Atacama Desert

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

Complete plastome sequence of Lysimachia congestiflora Hemsl. a medicinal and ornamental species in Southern China

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