De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis DOI Creative Commons
Hideki Hirakawa, Katsuhiko Sumitomo,

Tamotsu Hisamatsu

et al.

DNA Research, Journal Year: 2019, Volume and Issue: 26(3), P. 195 - 203

Published: Jan. 2, 2019

Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x 54) and large size. The diploid Chrysanthemum seticuspe often used as model cultivated chrysanthemum, since two species are closely related. To expand our knowledge we here performed de novo whole-genome assembly in C. using Illumina sequencing platform. XMRS10, accession developed by five generations self-crossing from self-compatible strain, AEV2, was for sequencing. 2.72 Gb assembled sequences (CSE_r1.0), consisting 354,212 scaffolds, covered 89.0% 3.06 estimated k-mer analysis. N50 length scaffolds 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on sequences, linkage map construction, gene discovery comparative analyses chrysanthemum. generated revealed skewed regions segregation AEV2 genome. In analysis, candidate flowering-related newly found CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification annotation × showed that applicable to genetic analysis chrysanthemums. herein expected contribute future studies. addition, approach demonstrated usefulness short-read importance choosing an appropriate next technology purpose post-genome

Language: Английский

Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data DOI
Xingtan Zhang, Shengcheng Zhang, Qian Zhao

et al.

Nature Plants, Journal Year: 2019, Volume and Issue: 5(8), P. 833 - 845

Published: Aug. 5, 2019

Language: Английский

Citations

461
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps DOI
Caroline Belser, Benjamin Istace, Erwan Denis

et al.

Nature Plants, Journal Year: 2018, Volume and Issue: 4(11), P. 879 - 887

Published: Oct. 24, 2018

Language: Английский

Citations

377
Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms DOI Creative Commons
Ren Ren, Haifeng Wang, Chunce Guo

et al.

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(3), P. 414 - 428

Published: Jan. 6, 2018

Language: Английский

Citations

313
Genome editing of upstream open reading frames enables translational control in plants DOI
Huawei Zhang, Xiaomin Si, Xiang Ji

et al.

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(9), P. 894 - 898

Published: Aug. 6, 2018

Language: Английский

Citations

292
The alternative reality of plant mitochondrial DNA: One ring does not rule them all DOI Creative Commons
Alexander Kozik, Beth A. Rowan, Dean Lavelle

et al.

PLoS Genetics, Journal Year: 2019, Volume and Issue: 15(8), P. e1008373 - e1008373

Published: Aug. 30, 2019

Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across broad community of life scientists that genome-sized molecules primary form plant DNA, despite understanding by researchers this is an inaccurate outdated concept. Many have one or more pairs large repeats can act sites for inter- intramolecular recombination, leading to multiple alternative arrangements (isoforms). Most been using methods unable capture complete spectrum isoforms within a species, incomplete inference their structure recombinational activity. To document investigate underlying reasons structural diversity in we used long-read (PacBio) short-read (Illumina) sequencing data assemble compare domesticated (Lactuca sativa) wild (L. saligna L. serriola) lettuce species. We characterized comprehensive, complex set each species compared genome structures between Physical analysis sativa mtDNA fluorescence microscopy revealed variety linear, branched, structures. The serriola were identical sequence arrangement differed substantially from saligna, indicating did not change during domestication. From our data, infer recombination occurs at all sizes variable frequencies. differences two other Lactuca be largely explained rare events rearranged structure. Our demonstrate representations simple, accurate descriptions true nature reality DNA complex, dynamic mixture forms.

Language: Английский

Citations

275
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing DOI Creative Commons
Maximilian Schmidt, Alexander Vogel, Alisandra K. Denton

et al.

The Plant Cell, Journal Year: 2017, Volume and Issue: 29(10), P. 2336 - 2348

Published: Oct. 1, 2017

Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior this, sequencing was mainly used analyze microbial samples. Here, we describe the generation a comprehensive data set with median read length 11,979 bp for self-compatible accession wild tomato species Solanum pennellii We assembly its genome contig N50 2.5 MB. The pipeline comprised initial correction Canu and SMARTdenovo. resulting raw nanopore-based de novo is structurally highly similar that reference S. LA716 but has high error rate rich homopolymer deletions. After polishing Illumina reads, obtained an <0.02% when assessed versus same gene completeness 96.53%, slightly surpassing Taken together, our indicate such long can be affordably assemble gigabase-sized plant genomes.

Language: Английский

Citations

206
The Chrysanthemum nankingense Genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits DOI Creative Commons
Chi Song, Yifei Liu, Aiping Song

et al.

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(12), P. 1482 - 1491

Published: Oct. 18, 2018

Language: Английский

Citations

185
Current achievements and future prospects in the genetic breeding of chrysanthemum: a review DOI Creative Commons
Jiangshuo Su, Jiafu Jiang, Fei Zhang

et al.

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: Oct. 1, 2019

Abstract Chrysanthemum ( morifolium Ramat.) is a leading flower with applied value worldwide. Developing new chrysanthemum cultivars novel characteristics such as colors and shapes, plant architectures, flowering times, postharvest quality, biotic abiotic stress tolerance in time- cost-efficient manner the ultimate goal for breeders. Various breeding strategies have been employed to improve aforementioned traits, ranging from conventional techniques, including crossbreeding mutation breeding, series of molecular methods, transgenic technology, genome editing, marker-assisted selection (MAS). In addition, recent extensive advances high-throughput technologies, especially genomics, transcriptomics, proteomics, metabolomics, microbiomics, which are collectively referred omics platforms, led collection substantial amounts data. Integration these data phenotypic information will enable identification genes/pathways responsible important traits. Several attempts made use emerging methods aim accelerating chrysanthemum. However, applying findings studies practical remains considerable challenge, primarily due high heterozygosity polyploidy species. This review summarizes achievements modern technologies discusses their future applications improving agronomic horticultural

Language: Английский

Citations

165
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce DOI
Wei Tong,

R. van Treuren,

Xinjiang Liu

et al.

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(5), P. 752 - 760

Published: April 12, 2021

Language: Английский

Citations

112
Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield DOI Creative Commons
Baosheng Liao, Xiaofeng Shen, Xiang Li

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(8), P. 1310 - 1328

Published: June 1, 2022

Language: Английский

Citations

72