Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(8), P. 1248 - 1258

Published: July 18, 2022

Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes many crops have been generated, such work in has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing Hi-C technologies, we generated reference-quality genome assembly hulless common oat, comprising 21 pseudomolecules with total length 10.76 Gb contig N50 75.27 Mb. We also produced assemblies for diploid tetraploid Avena ancestors, which enabled the identification subgenomes provided insights into chromosomal evolution. The origin hexaploid inferred from whole-genome sequencing, chloroplast transcriptome different species. These findings high-quality presented here will facilitate full use genetic resources accelerate improvement.

Language: Английский

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Involvement of dehydrin proteins in mitigating the negative effects of drought stress in plants

Plant Cell Reports, Journal Year: 2021, Volume and Issue: 41(3), P. 519 - 533

Published: May 31, 2021

Language: Английский

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Fullerenol regulates oxidative stress and tissue ionic homeostasis in spring wheat to improve net-primary productivity under salt-stress

Ecotoxicology and Environmental Safety, Journal Year: 2021, Volume and Issue: 211, P. 111901 - 111901

Published: Jan. 14, 2021

The effects of fullerenol nanopriming (0, 10, 40, 80 and 120 nM concentration) on salt stressed-wheat (0 150 mM NaCl) were investigated under natural conditions. Salinity resulted in a shift wheat growth pattern the form LAR (+ 40.9% increase) RGR 13.4% while decreased NAR (− 31.7%). It also disturbed shoot root biomass, ion uptake reduced chlorophyll contents. Despite increase enzyme activities, higher ROS generation 48.1% O2− anion; + 62.2% H2O2) lipid peroxidation 40.8% MDA) detected salt-stressed plants. Possibly, increases activities not up to level completely counteract salinity induced oxidative stress. Nanopriming with improved 8.77% 23.2%), metabolism indicators Hydropriming treatment promoted recovery by 21.9% than control Compared Na+ ions, improvements relative concentrations K+, Ca2+ P recorded along soluble sugars amino acids, which osmotic balance. These biochemical modifications contributed grain yield attributes (+11.8% 18.3% 100 grain-weight) stressed control. 12.6%. Above all, harvested seeds from treated plants showed better germination seedlings traits. Conclusively, we report non-toxic, growth-promoting nanoparticles crop as way forward; suggest its exogenous application recover productivity saline environments.

Language: Английский

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Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: June 24, 2022

Members of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit kidney spleen among patients. However, phylogenetic relationships intrageneric taxonomy within long controversial because complexity their morphological variations lack high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering related families. In present study, complete cp 26 species Trib. Polygonateae were de novo assembled characterized; all exhibited a conserved quadripartite structure, is, two inverted repeats (IR) containing most ribosomal RNA genes, unique regions, large single sequence (LSC) small (SSC). A total 8 highly variable regions (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, trnC-GCA-petN) might be useful as potential markers identifying identified. clock analysis results showed divergence time occur at ∼14.71 Ma, verticillate leaf ancestral state this genus. Moreover, based on 88 genomes strongly supported monophyly Polygonatum. also suggested Heteropolygonatum may sister group Polygonatum, but Disporopsis, Maianthemum, Disporum diverged earlier. This study provides valuable information further identification, evolution, research

Language: Английский

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Insights into Phylogeny, Taxonomy, Origins and Evolution of Crataegus and Mespilus, Based on Comparative Chloroplast Genome Analysis

Genes, Journal Year: 2025, Volume and Issue: 16(2), P. 204 - 204

Published: Feb. 7, 2025

Hawthorns (Crataegus L.) are widely distributed and well known for their medicinal properties health benefits. Nevertheless, the phylogenetic relationships among Crataegus native to China remain unclear. Additionally, no consensus exists on origin evolution of Crataegus, relationship between Mespilus is Here, we sequenced 20 chloroplast (cp) genomes (19 from 1 Mespilus) combined them with 2 existing cp investigate relationships, divergence times biogeographic history Crataegus. Four hypervariable loci emerged newly genomes. The results indicated that 14 Chinese species analyzed clustered into two clades. One clade North American grouped together, while other European species. Our favor recognizing as one genus. Molecular dating analyses showed originated in Southwest during early Oligocene, approximately 30.23 Ma ago. Transoceanic migration East Asian across Bering land bridge led development species, whereas westward ancestors C. songarica drove formation cuneata may represent earliest lineage uplift Qinghai-Tibet Plateau (QTP) monsoon system have south-western migrate toward northeast, giving rise This study offers crucial insights origins proposes an evolutionary model

Language: Английский

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Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 11

Published: Jan. 27, 2021

The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. the four newly sequenced plastomes that represent all three subgenera , detected (1) two independent relocations same five genes ( trnV-UAC - rbcL ) from typically posterior part large single-copy (LSC) region front, downstream either atpH gene saxicola or trnK-UUU both davidii and hsiaowutaishanensis ; (2) relocation rps16 LSC inverted repeat (IR) adunca (3) uniform inversion an 11–14 kb segment ndhB trnR-ACG IR species (the below); (4) expansions (>10 kb) into small (SSC) corresponding contractions SSC region; (5) pseudogenizations losses 13 accD clpP 11 ndh genes). addition, also found exhibited elevated GC content intergenic regions high number dispersed repeats. Phylogenomic analyses generated well-supported topology was consistent result previous studies based on DNA markers but contradicted morphological character-based taxonomy some extent. This study provided insights evolution throughout will value for further taxonomy, phylogeny, .

Language: Английский

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Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

BMC Plant Biology, Journal Year: 2021, Volume and Issue: 21(1)

Published: Nov. 23, 2021

Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in each possess 50 or more species, including Globba (100), Hedychium ( > 80), Kaempferia (50) Zingiber (150). Despite agricultural, medicinal horticultural importance these genomic resources suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled analyzed ten complete chloroplast genomes from nine species Zingiberoideae: lancangensis , marantina multiflora schomburgkii var. angustata coccineum neocarneum rotunda ‘Red Leaf’, ‘Silver Diamonds’ recurvatum . These (size range 162,630–163,968 bp) typical quadripartite structures that consist single copy (LSC, 87,172–88,632 bp), small (SSC, 15,393–15,917 pair inverted repeats (IRs, 29,673–29,833 bp). The contain 111–113 different genes, 79 protein coding 28–30 tRNAs 4 rRNA genes. dynamics genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence long exhibit similarities, with slight differences observed among genomes. Further comparative analysis seventeen related 12 divergent hotspots identified. Positive selection 14 accD ccsA ndhA ndhB psbJ rbcL rpl20 rpoC1 rpoC2 rps12 rps18 ycf1 ycf2 ycf4. Phylogenetic analyses, based on chloroplast-derived single-nucleotide polymorphism data, strongly support Curcuma I + “ clade” consisting II, form nested evolutionary relationship Zingiberoideae. Conclusions Our study provides detailed information genomes, representing valuable resource future studies seek to understand identified can be used development phylogenetic inference identification closely within four

Language: Английский

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Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 3, 2023

The subgenus Cerasus , one of the most important groups in genus Prunus sensu lato comprises over 100 species; however, taxonomic classification and phylogenetic relationships remain controversial. Therefore, it is necessary to reconstruct tree for known species. Here, we report chloroplast (cp) genome sequences 11 species provide insight into evolution plastome. cp genomes (157,571–158,830 bp) displayed a typical quadripartite circular structure. plastomes contain 115 unique genes, including 80 protein-coding four ribosomal RNAs, 31 transfer RNAs. Twenty genes were found be duplicated inverted repeats as well at boundary. conserved non-coding showed significant divergence compared with coding regions. We 12 14 intergenic regions higher nucleotide diversity more polymorphic sites, matK rps16 rbcL - trnQ petN psbM trnL trnF . During plastome evolution, codon profile has been strongly biased toward use A/T third base, leucine isoleucine codons appear frequently. identified strong purifying selection on rpoA cemA atpA petB genes; whereas ccsA rps19 rpoC2 ycf2 ndhI signature possible positive during course evolution. In addition, further analyzed these 57 other congenic related species.Through reconstructing phylogeny tree, that true cherry similar flora China forming distinct group, from which P. mahaleb was separated an independent subclade. Microcerasus genetically closer Amygdalus Armeniaca ( stricto ) than members cherry, japonica tomentosa closely triloba pedunculata However, tianshanica formed clade cerasus fruticosa × canescens ‘Gisela 6’, avium group. These results new insights along potential molecular markers candidate DNA barcodes phylogeographic analyses

Language: Английский

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The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis

Genes, Journal Year: 2022, Volume and Issue: 13(2), P. 369 - 369

Published: Feb. 18, 2022

, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of

Language: Английский

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Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Oct. 5, 2022

Paraboea (Gesneriaceae) distributed in the karst areas of South and Southwest China Southeast Asia, is an ideal genus to study phylogeny adaptive evolution plants. In this study, complete chloroplast genomes twelve species were sequenced analyzed. Twelve ranged size from 153166 154245 bp. Each genome had a typical quartile structure, relatively conserved type number gene components, including 131 genes which are composed 87 protein coding genes, 36 transfer RNAs 8 ribosomal RNAs. A total 600 simple sequence repeats 389 non-overlapped obtained genomes. We found ten divergent regions (trnH-GUG-psbA, trnM-CAU, trnC-GCA, atpF-atpH, ycf1, trnK-UUU-rps16, rps15, petL, trnS-GCU-trnR-UCU psaJ-rpl33) among 12 be potential molecular markers. phylogenetic tree 31 Gesneriaceae plants species, all clustered clade confirmed monophyly Paraboea. Nine with positive selection sites detected, most related photosynthesis synthesis, might played crucial roles adaptability diverse environments. These findings valuable for further

Language: Английский

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