Nature Climate Change, Journal Year: 2017, Volume and Issue: 8(1), P. 29 - 37
Published: Dec. 20, 2017
Language: Английский
Genome biology, Journal Year: 2019, Volume and Issue: 20(1)
Published: Feb. 21, 2019
Abstract Background The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences gene duplication in a range taxa, unravel common principles underlying duplicate retention. Results We survey 141 sequenced genomes elucidate duplication, processes central the evolution biodiversity. develop pipeline named DupGen_finder identify different modes plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed differ abundance, selection pressure, expression divergence, conversion rate among genomes. number WGD-derived genes decreases exponentially with increasing age events—transposed duplication- duplication-derived declined parallel. In contrast, frequency tandem proximal duplications showed no significant decrease over time, providing continuous supply variants available for adaptation continuously changing environments. Moreover, duplicates experienced stronger selective pressure than formed by other evolved toward biased functional roles involved self-defense. pairs peaking shortly after polyploidization. To platform accessing duplicated plants, we constructed Plant Duplicate Gene Database. Conclusions comprehensive landscape across kingdom comparing genomes, which provides solid foundation further investigation dynamic genes.
Language: Английский
Citations
811
Nature, Journal Year: 2018, Volume and Issue: 554(7692), P. 311 - 316
Published: Feb. 1, 2018
The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses 60 accessions representing diverse germ plasms, propose that diversified during late Miocene epoch through a rapid southeast Asian radiation correlates with marked weakening monsoons. A second enabled by migration across Wallace line gave rise to Australian limes in early Pliocene epoch. Further identification hybrids admixed genomes provides insights into genealogy major commercial cultivars citrus. Among mandarins sweet orange, find extensive network relatedness illuminates domestication these groups. Widespread pummelo admixture among its correlation size acidity suggests plausible role introgression selection palatable mandarins. This work new evolutionary framework for Citrus. origin, evolution Citrus important wild varieties. fruits are one yet relationships species remain uncertain. Daniel Rokhsar, Manuel Talon colleagues analyse represent range including 30 newly sequenced genomes. They characterize diversity at level identify interspecific admixtures—genetic mixing between previously isolated populations—that could be result human activities such as agriculture. authors 10 progenitor suggest originated Asia, diversifying correlated changing climate, also oranges, showing complex history
Language: Английский
Citations
697
Genome biology, Journal Year: 2016, Volume and Issue: 17(1)
Published: Sept. 23, 2016
DNA methylation is an important feature of plant epigenomes, involved in the formation heterochromatin and affecting gene expression. Extensive variation patterns within a species has been uncovered from studies natural variation. However, extent to which varies between flowering still unclear. To understand genomic patterning across species, we compared single base resolution methylomes 34 diverse angiosperm species.By analyzing whole-genome bisulfite sequencing data phylogenetic context, it becomes clear that there extensive throughout angiosperms body methylation, euchromatic silencing transposons repeats, as well heterochromatic transposons. The Brassicaceae have reduced CHG levels also or loss CG methylation. Poaceae are characterized by lack reduction CHH enrichment genic regions. Furthermore, low observed number especially clonally propagated species.These results reveal show broadly reflection evolutionary life histories species.
Language: Английский
Citations
507
Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)
Published: Nov. 14, 2018
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome thought to play an important role in promoting citrus growth and health. Here, we report comprehensive analysis of the structural functional composition microbiome. We use both amplicon deep shotgun metagenomic sequencing bulk soil samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria Bacteroidetes. The core comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax Paraburkholderia, some which are potential plant beneficial microbes. also identify over-represented microbial traits mediating plant-microbe microbe-microbe interactions, nutrition acquisition promotion rhizosphere. results provide valuable information guide isolation culturing and, potentially, harness power improve production
Language: Английский
Citations
424
Nature Genetics, Journal Year: 2017, Volume and Issue: 49(5), P. 765 - 772
Published: April 10, 2017
The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature modern citrus. Here we de novo sequenced and comprehensively studied the genomes four representative citrus species. Additionally, 100 accessions primitive, wild cultivated Comparative population analysis suggested that genomic regions harboring energy- reproduction-associated genes are probably under selection in We also narrowed genetic locus responsible for polyembryony, form apomixis, an 80-kb region containing 11 candidate genes. One these, CitRWP, is expressed at higher levels ovules polyembryonic cultivars. found miniature inverted-repeat transposable element insertion promoter CitRWP cosegregated with polyembryony. This study provides new insights into apomixis constitutes promising resource mining agriculturally important
Language: Английский
Citations
407
Genome biology, Journal Year: 2016, Volume and Issue: 17(1)
Published: Feb. 29, 2016
We have witnessed an explosion in our understanding of the evolution and structure plant genomes recent years. Here, we highlight three important emergent realizations: (1) that evolutionary history all contains multiple, cyclical episodes whole-genome doubling were followed by myriad fractionation processes; (2) vast majority variation genome size reflects dynamics proliferation loss lineage-specific transposable elements; (3) various classes small RNAs help shape genomic architecture function. illustrate ways which these organism-level molecular genetic processes can be used for crop improvement.
Language: Английский
Citations
391
Nature Biotechnology, Journal Year: 2016, Volume and Issue: 34(5), P. 562 - 570
Published: April 18, 2016
Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia is now grown in tropical regions worldwide. Here we provide high-quality genome assembly cassava with improved contiguity, linkage, completeness; almost 97% genes are anchored to chromosomes. We find that paleotetraploidy shared related rubber tree Hevea, providing resource comparative studies. also sequence global collection 58 Manihot accessions, including cultivated accessions species such as Ceará or India (M. glaziovii), genotype 268 African varieties. widespread interspecific admixture, detect genetic signature past breeding programs. As clonally propagated crop, especially vulnerable pathogens abiotic stresses. This genomic will inform future genome-enabled efforts improve this staple crop.
Language: Английский
Citations
383
Plant Biotechnology Journal, Journal Year: 2015, Volume and Issue: 14(4), P. 1070 - 1085
Published: Aug. 26, 2015
Plant breeders require access to new genetic diversity satisfy the demands of a growing human population for more food that can be produced in variable or changing climate and deliver high-quality with nutritional health benefits demanded by consumers. The close relatives domesticated plants, crop wild (CWRs), represent practical gene pool use plant breeders. Genomics CWR generates data support expand plants. Advances DNA sequencing technology are enabling efficient their increased improvement. As genomes major species is completed, attention has shifted analysis wider crops including CWR. A combination de novo resequencing required efficiently explore useful variation Analysis nuclear genome, transcriptome maternal (chloroplast mitochondrial) genome facilitating Genome results discovery alleles identification regions which been lost domestication bottlenecks. Targeting high priority will maximize contribution Coordination global efforts apply genomics potential accelerate conservation biodiversity essential sustainability agriculture production.
Language: Английский
Citations
363
BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)
Published: March 11, 2017
The availability of the peach genome sequence has fostered relevant research in and related Prunus species enabling identification genes underlying important horticultural traits as well development advanced tools for genetic genomic analyses. first release (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions mapped sequences (96%) base accuracy (99.96%). aim this work was to improve quality by increasing portion oriented sequences, correcting misassemblies improving using high-throughput linkage mapping deep resequencing approaches. Four maps 3,576 molecular markers were used (from 96.0% 85.6% Peach v1.0 99.2% 98.2% v2.0, respectively) enabled more detailed discernible (10.4 Mb total). approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) 1347 indels. Moreover, assembled NGS contigs closing 212 gaps an improvement contig 19.2%. improved v2.0) represents valuable tool analysis diversity, domestication, vehicle species. phylogenetic position absence recent whole duplication (WGD) events make pivotal comparative genomics studies aiming at elucidating plant speciation diversification processes.
Language: Английский
Citations
354
Molecular Biology and Evolution, Journal Year: 2015, Volume and Issue: 32(8), P. 2015 - 2035
Published: April 14, 2015
Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because its commercial relevance, origin citrus species and history domestication still remain an open question. Here, we present a phylogenetic analysis chloroplast genomes 34 genotypes which constitutes comprehensive detailed study to date on evolution variability Citrus. A statistical model was used estimate divergence times between major groups. Additionally, complete map across genome different produced, including single nucleotide variants, heteroplasmic positions, indels (insertions deletions), large structural variants. The distribution all these variants provided further independent support phylogeny obtained. An unexpected finding high level heteroplasmy found in several analyzed genomes. use DNA not only paves way for better understanding relationships within but also provides original insights into other elusive evolutionary processes, such as inheritance, heteroplasmy, gene selection.
Language: Английский
Citations
293