Toward finally unraveling the phylogenetic relationships of Juncaceae with respect to another cyperid family, Cyperaceae

Brožová, Viktorie; Proćków, Jarosław; Drábková, Lenka Záveská

doi:10.1016/j.ympev.2022.107588

Cited by 9 publications

(25 citation statements)

References 75 publications

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“…The spikelets of Poaceae and Cyperaceae were similar. Chromosomes and pollen morphology indicate a close relationship between Cyperaceae and Juncaceae, while phylogenetic analysis suggests that Cyperaceae possesses a closer genetic relationship with Juncaceae and a farther relationship with Poaceae [ 51 , 52 ]. This study also demonstrated this evolutionary relationship by constructing a phylogenetic tree based on shared genes between mitochondria and chloroplasts.…”

Section: Discussionmentioning

confidence: 99%

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

Miao,

Yang,

et al. 2024

BMC Plant Biol

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Background Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. Results We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. Conclusion We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.

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Section: Discussionmentioning

confidence: 99%

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

Miao,

Yang,

et al. 2024

BMC Plant Biol

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“…If a family or genus has only one representative in the tree, the branch is split to represent taxonomic levels and new species are added at corresponding points of this split (see [62]), reducing the PD. Therefore, it is advisable to work on more detailed phylogenies for high Andean species, such as the phylogeny proposed by Brozova et al [63] for Juncaceae and Cyperaceae, a phylogeny that has been criticized by some authors (see [64]).…”

Section: Phylogenetic Diversitymentioning

confidence: 99%

Environmental Filters Structure Cushion Bogs’ Floristic Composition along the Southern South American Latitudinal Gradient

Figueroa-Ponce,

Hinojosa

2024

Preprint

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In southern South America, zonal flora, defined by macroclimatic conditions, is strongly influenced by an aridity filter near 29°S. Cushion bogs, high-altitude wetlands along the Andes, display homogeneous flora with cushion species dominance, contrasting with zonal vegetation. Despite being influenced by microclimatic conditions, these ecosystems experience varied environmental effects. This study identifies environmental filters affecting bog communities along a broad-scale latitudinal gradient from 15°S to 42°S. We analyzed 420 bogs and 284 species across three macroclimatic regions with distinct summer, winter, and transitional arid rainfall regimes. Using variance partitioning and membership-based regionalization models, we examined the impacts of climatic, edaphic, and spatial variables on beta diversity. We also assessed species' niche overlap and the influence of environmental filters on the communities' phylogenetic diversity. Results show that species turnover and niche overlap vary with macroclimatic differences, delineating three distinct regions. Notably, phylogenetic clustering in the driest part of the gradient (23°S —24°S) highlights the impact of the environmental filter. Aridity and temperature variations at a broad scale serve as environmental filters shaping the composition of bog communities across southern South America.

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“…Juncus is the largest genus and includes ~300 species (Balslev, 2018) and two major subgenera, Agathryon and Juncus (Drábková, 2010; Drábková et al, 2006). Although many species of Juncaceae have been included in phylogenetic studies using plastid gene sequences and the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat (Table S1; Brožová et al, 2022; Drábková, 2010; Drábková et al, 2006), species relationships within Juncus remain unresolved. Brožová et al (2022) recently incorporated rbcL , trnL , trnL ‐ trnF and ITS1–5.8–ITS2 regions to reorganize Juncus into seven distinct genera: Juncus , Verojuncus , Juncinella , Alpinojuncus , Australojuncus , Boreojuncus and Agathryon .…”

Section: Introductionmentioning

confidence: 99%

“…Not many plastome structures have been reported for Juncus ( s.l .). To avoid confusion regarding Juncus species names, we did not adopt the generic classification of Brožová et al (2022) in the present investigation because a more comprehensive study with more markers is necessary to justify this reranking. Plastomes of just eight Juncus species are publicly available in GenBank (Lu et al, 2021; Wu et al, 2021), but there has been little investigation of how the plastome itself has changed structurally in Juncus ( s.l .).…”

Section: Introductionmentioning

confidence: 99%

Plastid Genome Assembly Using Long‐read data

Zhou

Armijos

Lee

et al. 2023

Molecular Ecology Resources

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Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single‐copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short‐read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single‐molecule, long‐read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long‐read data. We generated a pipeline, plastid Genome Assembly Using Long‐read data (ptGAUL), to address the problem of plastome assembly using long‐read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long‐read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul.

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Toward finally unraveling the phylogenetic relationships of Juncaceae with respect to another cyperid family, Cyperaceae

Cited by 9 publications

References 75 publications

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

Environmental Filters Structure Cushion Bogs’ Floristic Composition along the Southern South American Latitudinal Gradient

Plastid Genome Assembly Using Long‐read data

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