Charting the genomic landscape of seed-free plants

Szövényi, Péter; Gunadi, Andika; Li, Fay‐Wei

doi:10.1038/s41477-021-00888-z

Cited by 55 publications

(74 citation statements)

References 172 publications

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“…In addition, we conducted an extensive literature search to identify additional genome assemblies not deposited in GenBank. To do so, we took advantage of review papers summarizing plant genome assemblies [23][24][25][26] and other datasets such as PlaBi database (www.plabipd.de), Phytozome (https://phytozome.jgi.doe.gov/), Fernbase (https://www.fernbase.org/), and (https://en.wikipedia.org/wiki/List_of_sequenced_plant_genomes). We cross referenced these datasets against NCBI to develop a nonredundant but comprehensive list of plant genome assemblies.…”

Section: Discussionmentioning

confidence: 99%

“…and two hornwort (both Anthoceros spp.) genome assemblies that are not yet available on GenBank 23 . Diploid species are also statistically overrepresented in terms of genome availability (Fig.…”

Section: Introductionmentioning

confidence: 99%

“…Here, we provide a high-level perspective on the first 20 years of plant genome sequencing. We describe the taxonomic distribution of sequencing efforts and build on previous estimates of genome availability and quality [23][24][25][26] . We show that an impressive and growing number of plant genome assemblies are now publicly available, that quality has greatly improved in concert with the rise of long-read sequencing, but that substantial taxonomic gaps exist.…”

Section: Introductionmentioning

confidence: 99%

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Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

Hotaling

Frandsen

VanBuren

2021

Preprint

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The field of plant genomics has grown rapidly in the past 20 years, leading to dramatic increases in both the quantity and quality of publicly available genomic resources. With an ever-expanding wealth of genomic data from an increasingly diverse set of taxa, unprecedented potential exists to better understand the evolution and genome biology of plants. Here, we provide a contemporary view of plant genomics, including analyses on the quality of existing plant genome assemblies, the taxonomic distribution of sequenced species, and how national participation has influenced the fields development. We show that genome quality has increased dramatically in recent years, that substantial taxonomic gaps exist, and that the field has been dominated by affluent nations in the Global North, despite a wide geographic distribution of sequenced species. We identify multiple inconsistencies between the range of focal species and the national affiliation of the researchers studying the plants, which we argue are rooted in colonialism--both past and present. Falling sequencing costs paired with widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps, and, most importantly, empower a more global plant genomics community.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

Hotaling

Frandsen

VanBuren

2021

Preprint

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“…The identification of progenitors of lignin biosynthetic genes in bryophytes provides new insights into the origin of lignin biosynthesis (Kriegshauser et al, 2021). The recent progress on genome sequencing of Charophyte algae, bryophytes, lycophytes, and ferns have also provided unprecedented opportunities to study the origin of phenylpropanoid biosynthetic pathway (Szövényi et al, 2021).…”

Section: Perspectives On the Origin And Evolution Of Lignin Biosynthesis In Plantsmentioning

confidence: 99%

Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants

et al. 2021

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The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.

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“…Land plants evolved from a charophycean algal ancestor approximately 470-515 million years ago, and consist of two monophyletic lineages: tracheophytes (vascular plants) and bryophytes (i.e., mosses, liverworts, and hornworts) (Szövényi et al, 2021). Bryophytes are, perhaps, the oldest lineage of land plants to form stable long-lasting endosymbiotic associations with nitrogen-fixing bacteria, in this case oxygenic photoautotrophic cyanobacteria (Sprent and Raven, 1985).…”

Section: Introductionmentioning

confidence: 99%

Nostoc talks back: Temporal patterns of differential gene expression during establishment of the Anthoceros-Nostoc symbiosis

Chatterjee

Schafran

et al. 2021

Preprint

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Endosymbiotic association between hornworts and dinitrogen-fixing cyanobacteria form when the plant is limited for combined nitrogen (N). We generated RNA-Seq data to examine the temporal gene expression patterns during culture of N-starved Anthoceros punctatus in the absence and presence of the symbiotically competent cyanobacterium Nostoc punctiforme. Symbiotic nitrogenase activity commenced within 5 days of coculture reaching a maximal by 14 days. In symbiont-free gametophytes, chlorophyll content, chlorophyll fluorescence characteristics and transcription of genes encoding light harvesting and reaction center proteins, as well as the small subunit of ribulose-bisphosphate-carboxylase/oxygenase, were downregulated. The downregulation was complemented in a temporal pattern corresponding to the N. punctiforme provision of N2-derived ammonium. The impairment and complementation of photosynthesis was the most distinctive response of A. punctatus to N-starvation. Increases in transcription of ammonium and nitrate transporters and their N. punctiforme-dependent complementation was also observed. The temporal patterns of differential gene expression indicated N. punctiforme transmits signals to A. punctatus both prior to, and after its provision of fixed N. This is the only known temporal transcriptomic study during establishment of a symbiotic nitrogen-fixing association in this monophyletic evolutionary lineage of land plants.HighlightsTemporal RNA-Seq analysis revealed how symbiotic cyanobacteria impact plant partners’ global gene expression and elucidated the nature of bidirectional communications between the partners

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Charting the genomic landscape of seed-free plants

Cited by 55 publications

References 172 publications

Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants

Nostoc talks back: Temporal patterns of differential gene expression during establishment of the Anthoceros-Nostoc symbiosis

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