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Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

ABSTRACT: Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

SUBMITTER: Mitros T

PROVIDER: S-EPMC7595124 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

Mitros Therese T Session Adam M AM James Brandon T BT Wu Guohong Albert GA Belaffif Mohammad B MB Clark Lindsay V LV Shu Shengqiang S Dong Hongxu H Barling Adam A Holmes Jessica R JR Mattick Jessica E JE Bredeson Jessen V JV Liu Siyao S Farrar Kerrie K Głowacka Katarzyna K Jeżowski Stanisław S Barry Kerrie K Chae Won Byoung WB Juvik John A JA Gifford Justin J Oladeinde Adebosola A Yamada Toshihiko T Grimwood Jane J Putnam Nicholas H NH De Vega Jose J Barth Susanne S Klaas Manfred M Hodkinson Trevor T Li Laigeng L Jin Xiaoli X Peng Junhua J Yu Chang Yeon CY Heo Kweon K Yoo Ji Hye JH Ghimire Bimal Kumar BK Donnison Iain S IS Schmutz Jeremy J Hudson Matthew E ME Sacks Erik J EJ Moose Stephen P SP Swaminathan Kankshita K Rokhsar Daniel S DS

Nature communications 20201028 1

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allot ...[more]

PMID: 33116128

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Project description:BACKGROUND:The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS:We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size?=?415.8?Mb, scaffold N50?=?948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~?10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS:Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

Dataset Information

Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

Publications

Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

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