Genome-Wide Identification, Comprehensive Gene Feature, Evolution, and Expression Analysis of Plant Metal Tolerance Proteins in Tobacco Under Heavy Metal Toxicity DOI Creative Commons
Ji‐Kai Liu, Yongfeng Gao,

Yunlai Tang

et al.

Frontiers in Genetics, Journal Year: 2019, Volume and Issue: 10

Published: April 24, 2019

Plant metal tolerance proteins (MTPs) comprise a family of membrane divalent cation transporters that play essential roles in plant mineral nutrition maintenance and heavy stresses resistance. However, the evolutionary relationships biological functions MTP tobacco remain unclear. In present study, 26, 13 12 MTPs three main Nicotiana species (N. tabacum, N.sylvestris N. tomentosiformis) were identified, respectively, designated based on orthologous relationship to Arabiodopsis MTPs. The phylogenetic relationships, gene structures, chromosome distributions, conserved motifs domains NtMTPs systematic analyzed. According features, 26 classified into major substrate-specific groups (Zn-CDFs, Zn/Fe-CDFs Mn-CDFs) seven primary (1, 5, 6, 7, 8, 9 12). All contained modified signature sequence cation_efflux domain, whereas some them also harbored ZT_dimer. Evolutionary analysis showed NtMTP N.tabacum originated from its parental genome sylvestris tomentosiformis, further underwent lost expanded via one segmental duplication event. Moreover, prediction cis-acting elements microRNA target sites genes suggested diverse complex regulatory mechanisms control expression. Expression profile derived transcriptome data quantitative real-time PCR (qRT-PCR) tissue expression patterns same group similar but varied among groups, indicating growth development. addition, under toxicity, exhibited various responses either leaves or roots. 20 found response at least ion treatment roots, respectively. These results provided perspective evolution helpful for functional characterization genes.

Language: Английский

Plant Glandular Trichomes: Natural Cell Factories of High Biotechnological Interest DOI Open Access
Alexandre Huchelmann, Marc Boutry, Charles Hachez

et al.

PLANT PHYSIOLOGY, Journal Year: 2017, Volume and Issue: 175(1), P. 6 - 22

Published: July 19, 2017

Multicellular glandular trichomes are epidermal outgrowths characterized by the presence of a head made cells that have ability to secrete or store large quantities specialized metabolites. Our understanding transcriptional control trichome initiation and development is still in its infancy. This review points some central questions need be addressed better understand how such cell structures arise from plant protodermis. A key unique feature their synthesize amounts, relative size, limited number As such, they qualify as true factories, making them interesting targets for metabolic engineering. In this review, recent advances regarding terpene engineering highlighted, with special focus on tobacco (Nicotiana tabacum). particular, choice promoters drive transgene expression best ways sink existing pools precursors discussed. The bioavailability natural precursor molecules parameter controlled so-called cross talk between different biosynthetic pathways. highlighted exact nature extent only partially understood at present. future, awareness of, detailed knowledge on, biology metabolism will generate new leads tap largely unexploited potential resistance pests lead improved production metabolites high industrial pharmacological value.

Language: Английский

Citations

296
Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum DOI Creative Commons
Aiping Song, Jiangshuo Su, Haibin Wang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 11, 2023

Abstract Chrysanthemum ( morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum challenging due to its complex genetic background. Here, we report near-complete assembly annotation for C. comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative evolutionary analyses reveal whole-genome triplication (WGT) event shared by species approximately 6 million years ago (Mya) the possible lineage-specific polyploidization 3 Mya. Multilevel evidence suggests that likely segmental allopolyploid. Furthermore, combination genomics transcriptomics approaches demonstrate genome can be used identify genes underlying key traits. Phylogenetic analysis CmCCD4a traces flower colour breeding history cultivated chrysanthemum. Genomic resources generated from this study could help accelerate improvement.

Language: Английский

Citations

82
Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding DOI Creative Commons
Yaoyao Wu, Dawei Li, Yong Hu

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(11), P. 2313 - 2328.e15

Published: May 1, 2023

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to seed-reproducing diploid. Historical accumulation of deleterious mutations in genomes has hindered development elite inbred lines and hybrids. Utilizing whole-genome phylogeny 92 Solanaceae its sister clade species, we employ an evolutionary strategy identify mutations. The deep reveals genome-wide landscape highly constrained sites, comprising ∼2.4% genome. Based on diploid diversity panel, infer 367,499 variants, which 50% occur at non-coding 15% synonymous sites. Counterintuitively, with relatively high homozygous burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion inferred increases genomic-prediction accuracy yield by 24.7%. Our study generates insights into incidence properties their far-reaching consequences breeding.

Language: Английский

Citations

56
A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology DOI Creative Commons
Buddhini Ranawaka, Jiyuan An, Michał T. Lorenc

et al.

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

Citations

52
High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals DOI Creative Commons
Jubin Wang, Qingling Zhang, Jeffrey J. Tung

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(3), P. 423 - 437

Published: Jan. 24, 2024

Nicotiana tabacum and benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report the chromosome-level reference genome assemblies for N. with an estimated 99.5% 99.8% completeness, respectively. Sensitive transcription start termination site sequencing methods were developed accurate gene annotation tabacum. Comparative analyses revealed evidence parental origins chromosome structural changes, leading to hybrid formation each species. Interestingly, antiviral silencing genes RDR1, RDR6, DCL2, DCL3, AGO2 lost from one or both subgenomes benthamiana, while homeologs kept Furthermore, encodes fewer immune receptors signaling components than that These findings uncover possible reasons underlying hypersusceptible nature benthamiana. We user-friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) web server facilitate better use resources as well structure expression analyses.

Language: Английский

Citations

33
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis DOI Creative Commons
Amit Rai, Hideki Hirakawa, Ryo Nakabayashi

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 15, 2021

Abstract Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference phased genome Ophiorrhiza pumila , a camptothecin-producing medicinal plant, through an ordered multi-scaffolding experimental validation approach. With 21 gaps contig N50 18.49 Mb, is one the most complete plant assembled date. We also 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as origin MIA evolution. The emergence biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. before duplication Camptotheca acuminata identified here. Combining analysis, multi-omics metabolic gene-cluster propose working model for evolution, pangenome biosynthesis, will help establishing sustainable supply camptothecin.

Language: Английский

Citations

102
Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes DOI
Hyungtaek Jung, Christopher Winefield, Aureliano Bombarely

et al.

Trends in Plant Science, Journal Year: 2019, Volume and Issue: 24(8), P. 700 - 724

Published: June 14, 2019

Language: Английский

Citations

100
Genome Sequence and Analysis ofNicotiana benthamiana, the Model Plant for Interactions between Organisms DOI Creative Commons
Ken‐ichi Kurotani, Hideki Hirakawa, Kenta Shirasawa

et al.

Plant and Cell Physiology, Journal Year: 2023, Volume and Issue: 64(2), P. 248 - 257

Published: Feb. 1, 2023

Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains in research are highly susceptible to wide range of viruses. Accordingly, these subject pathology and plant-microbe interactions. terms plant-plant interactions, N. one plants that exhibit grafting affinity with from different families. Thus, good biology has been genome sequencing analyses many years. However, complex allopolyploid genome, its previous reference fragmented into 141,000 scaffolds. As result, molecular genetic analysis difficult perform. To improve this effort, de novo whole-genome assembly was performed Hifi reads, 1,668 contigs were generated total length 3.1 Gb. The 21 longest scaffolds, regarded pseudomolecules, contained 2.8-Gb sequence, occupying 95.6% assembled genome. A 57,583 high-confidence gene sequences predicted. Based on comparison structures between tabacum, found have more chromosomal rearrangements, reflecting age interspecific hybridization. verify accuracy annotations, cell wall modification genes involved analyzed, which revealed not only previously indeterminate untranslated region, intron open reading frame but also genomic locations their family genes. Owing improved annotation, would increasingly be accessible.

Language: Английский

Citations

37
Control of plastid inheritance by environmental and genetic factors DOI Creative Commons
Kin Pan Chung, Enrique Gonzalez-Duran, Stephanie Ruf

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(1), P. 68 - 80

Published: Jan. 16, 2023

The genomes of cytoplasmic organelles (mitochondria and plastids) are maternally inherited in most eukaryotes, thus excluding organellar from the benefits sexual reproduction recombination. mechanisms underlying maternal inheritance largely unknown. Here we demonstrate that two independently acting ensure plastid (chloroplast) genome. Conducting large-scale genetic screens for paternal transmission, discovered mild chilling stress during male gametogenesis leads to increased entry plastids into sperm cells strongly transmission. We further show is controlled by activity a genome-degrading exonuclease pollen maturation. Our data reveal (1) breaks down under specific environmental conditions, (2) an organelle exclusion mechanism genome degradation act concert prevent transmission genes (3) determined complex gene-environment interactions.

Language: Английский

Citations

28
Genome-wide identification and expression analysis of metal tolerance protein (MTP) gene family in soybean (Glycine max) under heavy metal stress DOI
Ahmed H. El‐Sappah, Manzar Abbas, Shabir A. Rather

et al.

Molecular Biology Reports, Journal Year: 2023, Volume and Issue: 50(4), P. 2975 - 2990

Published: Jan. 18, 2023

Language: Английский

Citations

27