How have orchid species diversified in the campos rupestres, Brazil? Fiorini et al. (2023) use genomic data sets and multidisciplinary approaches, including phylogenetics and population genomics, to ...investigate the diversity of Bulbophyllum. They demonstrate that geographic isolation alone does not explain diversification patterns in Bulbophyllum species throughout the sky forests. Some taxa show considerable evidence of gene flow, and lineages not previously identified as closely related could present a novel source of their genetic diversity.
Platystele ovatilabia (Ames & C. Schweinf.) Garay is illustrated, as the second of two Platystele species. The history, taxonomy and phylogenetic relationships of Platystele are discussed further.
Platystele misera (Lindl.) Garay is illustrated as the first of two species of Platystele Schltr., a genus of tiny Pleurothallid orchids from South and Central America. The ecology and distribution ...of Platystele are discussed, accompanied by brief notes on the cultivation of this species.
Summary
Platystele misera (Lindl.) Garay is illustrated as the first of two species of Platystele Schltr., a genus of tiny Pleurothallid orchids from South and Central America. The ecology and ...distribution of Platystele are discussed, accompanied by brief notes on the cultivation of this species.
Summary
Platystele ovatilabia (Ames & C. Schweinf.) Garay is illustrated, as the second of two Platystele species. The history, taxonomy and phylogenetic relationships of Platystele are discussed ...further.
Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C = 5.7 Gb. One of the most crucial ...factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as ‘junk’ DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression.
Summary
Amorphophallus ongsakulii Hett. & A.Galloway is illustrated from plants cultivated by the authors. Its ecology, distribution, and systematics are described, along with notes on cultivation.
Hyb-Seq for Flowering Plant Systematics Dodsworth, Steven; Pokorny, Lisa; Johnson, Matthew G. ...
Trends in plant science,
October 2019, 2019-10-00, 20191001, Letnik:
24, Številka:
10
Journal Article
Recenzirano
Odprti dostop
High-throughput DNA sequencing (HTS) presents great opportunities for plant systematics, yet genomic complexity needs to be reduced for HTS to be effectively applied. We highlight Hyb-Seq as a ...promising approach, especially in light of the recent development of probes enriching 353 low-copy nuclear genes from any flowering plant taxon.
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are ...fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this ...repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperme can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
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