Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

Shi, Junpeng; Ma, Xuxu; Zhang, Jihong; Zhou, Yingsi; Liu, Minxuan; Huang, Liangliang; Sun, Silong; Zhang, Xiangbo; Gao, Xiang; Zhan, Wei; Li, Pinghua; Wang, Lun; Lü, Ping; Zhao, Haiming; Song, Weibin; Lai, Jinsheng

doi:10.1038/s41467-018-07876-6

Cited by 97 publications

(73 citation statements)

References 65 publications

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“…The hybridization of two genomes can result in genome instability, extensive gene loss, and reshuffling. As a consequence, one sub-genome may evolve dominancy over the other sub-genome 23,30,32-34 . Using foxtail millet as a reference, the fonio A and B sub-genomes showed similar numbers of orthologous genes: 14,235 and 14,153 respectively.…”

Section: Resultsmentioning

confidence: 99%

“…BLASTP (E-value 1×10 −5 ) and MCScanX 83 (-s 10) were used to identify homoeologous relationships between the two sub-genomes of fonio accession CM05836 and orthologous relationships between CM05836 and Setaria italica 27 , Panicum miliaceum 34 , Panicum hallii 84 , Sorghum bicolor 75 , Zea mays 76 , Oryza sativa 77 , Brachypodium distachyon 85 , Hordeum vulgare 86 , Triticum aestivum 30 and Aegilops tauschii 87 . For all the comparisons, fonio sub-genomes A and B were analysed independently and only 1:1 and 1:2 relationships were retained according to the ploidy of the compared genomes.…”

Section: Methodsmentioning

confidence: 99%

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Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Abrouk

Ahmed

Cubry

et al. 2020

Preprint

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33Sustainable food production in the context of climate change necessitates diversification of 34 agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria 35 exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we 36 established high-quality genomic resources to facilitate fonio improvement through molecular 37 breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 38 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population 39 structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic 40 factors. Two genes associated with seed size and shattering showed signatures of selection. Most 41 known domestication genes from other cereal models however have not experienced strong 42 selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and 43 dry environments. 44 45 agriculture 1-3 . The Food and Agriculture Organization of the United Nations (FAO) stated that arid 50 and semi-arid regions are the most vulnerable environments to increasing uncertainties in regional 51 and global food production 4 . In most countries of Africa and the Middle East, agricultural 52 productivity will decline in the near future 4 , because of climate change, land degradation, and 53 groundwater depletion 5 . Agricultural selection, from the early steps of domestication to modern-54 day crop breeding, has resulted in a marked decrease in agrobiodiversity 6,7 . Today, three cereal 55 4 crops alone, bread wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa) account 56 for more than half of the globally consumed calories 8 . 57Many of today's major cereal crops, including rice and maize, originated in relatively humid 58 tropical and sub-tropical regions 9,10 . Although plant breeding has adapted the major cereal crops 59 to a wide range of climates and cultivation practices, there is limited genetic diversity within these 60 few plant species for cultivation in the most extreme environments. On the other hand, crop wild 61 relatives and orphan crops are often adapted to extreme environments and their utility to unlock 62 marginal lands for agriculture has recently regained interest 2,6,[11][12][13][14] . Current technological advances 63 in genomics and genome editing provide an opportunity to rapidly domesticate wild relatives and 64 to improve orphan crops 15,16 . De novo domestication of wild species or rapid improvement of semi-65 domesticated crops can be achieved in less than a decade by targeting a few key genes 6 . 66White fonio (Digitaria exilis (Kippist) Stapf) (Fig. 1) is an indigenous African millet species with 67 a great potential for agriculture in marginal environments 17,18 . Fonio is cultivated under a large 68 range of environmental conditions, from a tropical monsoon climate in western Guinea to a hot, 69 arid desert climate (BWh) in the Sahel zone. Some extra-early matur...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Abrouk

Ahmed

Cubry

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Although shotgun DNA sequencing (8) facilitated the assembly of a complete genome (9), the presence of tandemly repeated sequences, like gene copies, transposable elements, or satellite repeats of large genomes, prevents earlier developed sequencing platforms from delivering contiguous sequence information. PacBio with long reads (>10 kb) can cover sequence junctions between single repeats, such as retrotransposons, and can overcome assembly problems in terms of gap filling and repeat reconstruction in many plants, such as maize (10,11), Oropetium (12), quinoa (13), and broomcorn millet (14). To this end, we resequenced S. polyrhiza 7498 with ∼126-fold coverage of PacBio long reads, resulting in 411 contigs and an N50 length (a median of contig lengths) of 831 kb (15) Fig.…”

Section: Significancementioning

confidence: 99%

Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing ofSpirodela

Zhou

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retrotranspositions occur early in monocot evolution, featured with both prokaryote-like gene-rich regions and eukaryotic repeat islands. Protein-coding genes are reduced to 18,708 gene models supported by 492,435 high-quality full-length PacBio complementary DNA (cDNA) sequences. Different from land plants, the primitive architecture of Spirodela’s adventitious roots and lack of lateral roots and root hairs are consistent with dispensable functions of nutrient absorption. Disease-resistant genes encoding antimicrobial peptides and dirigent proteins are expanded by tandem duplications. Remarkably, disease-resistant genes are not only amplified, but also highly expressed, consistent with low levels of 24-nucleotide (nt) small interfering RNA (siRNA) that silence the immune system of land plants, thereby protecting Spirodela against a wide spectrum of pathogens and pests. The long-read sequence information not only sheds light on plant evolution and adaptation to the environment, but also facilitates applications in bioenergy and phytoremediation.

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“…However, no systematic study of the NAC family in broomcorn millet is available. The genome of broomcorn millet was recently published, providing an important resource for further molecular research in this species [57]. In addition, large RNA sequencing (RNA-seq) expression data from different tissues are also available [58].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

Shan

Jiang

et al. 2020

BMC Genomics

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Background: Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet.Results: In the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR. Conclusion: In this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance.

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Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

Cited by 97 publications

References 65 publications

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing ofSpirodela

Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

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