A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Nature Plants, Journal Year: 2023, Volume and Issue: 9(9), P. 1558 - 1571

Published: Aug. 10, 2023

Abstract Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness versatility, we have produced high-quality chromosome-level genome assemblies, coupled transcriptome, epigenome, microRNA transposable element datasets, for the ubiquitously used LAB strain related wild accession, QLD. In addition, single nucleotide polymorphism maps been two laboratory strains four accessions. Despite loss of five chromosomes from ancestral tetraploid, expansion intergenic regions, widespread segmental allopolyploidy, advanced diploidization evidence recent bursts Copia pseudovirus (Copia) mobility not seen in other genomes, subgenomes N. show large regions synteny across Solanaceae. QLD many genetic, metabolic phenotypic differences, including disparate RNA interference responses, but are highly interfertile amenable to editing both transient stable transformation. The LAB/QLD combination has potential be as useful Columbia-0/Landsberg errecta partnership, utilized early pioneering days Arabidopsis genomics today.

Language: Английский

---

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Nature Communications, Journal Year: 2016, Volume and Issue: 7(1)

Published: Nov. 8, 2016

Abstract Ipomoea is the largest genus in family Convolvulaceae. nil (Japanese morning glory) has been utilized as a model plant to study genetic basis of floricultural traits, with over 1,500 mutant lines. In present study, we have second- and third-generation-sequencing platforms, reported draft genome I. scaffold N50 2.88 Mb (contig 1.87 Mb), covering 98% 750 genome. Scaffolds 91.42% assembly are anchored 15 pseudo-chromosomes. The enabled identification cataloguing Tpn1 transposons, known major mutagen , analysing dwarf gene, CONTRACTED located on map published 1956. Comparative genomics suggested that whole duplication Convolvulaceae, distinct from recent Solanaceae event, occurred after divergence two sister families.

Language: Английский

---

The Genetics of Plant Metabolism

Annual Review of Genetics, Journal Year: 2017, Volume and Issue: 51(1), P. 287 - 310

Published: Sept. 6, 2017

Plant metabolic studies have traditionally focused on the role and regulation of enzymes catalyzing key reactions within specific pathways. Within past 20 years, reverse genetic approaches allowed direct determination effects deficiency, or surplus, a given protein biochemistry plant. In parallel, top-down also been taken, which rely screening broad, natural diversity for diversity. Here, we compare contrast various strategies that adopted to enhance our understanding metabolism. We detail how these enhanced both global aspects Finally, discuss such are providing important insights into evolution plant secondary

Language: Английский

---

Functional studies of transcription factors involved in plant defenses in the genomics era

Briefings in Functional Genomics, Journal Year: 2015, Volume and Issue: 14(4), P. 260 - 267

Published: April 2, 2015

Plant transcription factors (TFs) play roles in diverse biological processes including defense responses to pathogens. Here, we provide an overview of recent studies plant TFs with regard responses. innate immunity by regulating genes related pathogen-associated molecular pattern-triggered immunity, effector-triggered hormone signaling pathways and phytoalexin synthesis. Currently, genome-wide phylogenetic transcriptomic analyses are as important functional the study TFs. The integration genomics information knowledge obtained from provides new insights into regulation mechanisms well engineering crops improved resistance invading

Language: Английский

---

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Horticulture Research, Journal Year: 2018, Volume and Issue: 5(1)

Published: Jan. 12, 2018

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility this complex plant genomes is unproven. We evaluated purpose by 3.5-gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single library. Plant including pepper, are characterized long, highly similar repetitive sequences. Accordingly, significant effort used to ensure that sequenced homozygous and resulting haploid consensus. With phased approach, we targeted heterozygous F1 derived from wide cross assess ability derive both haplotypes characterize pungency gene large insertion/deletion. The Supernova software generated ordered, more contiguous sequence than all currently available C. annuum reference genomes. Over 83% final was anchored oriented using four publicly linkage maps. A comparison annotation conserved eukaryotic genes indicated completeness assembly. validity further demonstrated complete recovery 2.5-Kb insertion/deletion PUN1 locus in sample represents pungent nonpungent peppers, as well nearly full BUSCO2 set within each two haplotypes. most date which demonstrates library provides tool assemble This can provide an opportunity cost-effectively develop high-quality assemblies other plants compare structural differences through accurate haplotype reconstruction.

Language: Английский

---