The draft genomes of five agriculturally important African orphan crops

Chang, Yue; Liu, Min; Liao, Xuezhu; Sahu, Sunil Kumar; Fang, Yuan; Song, Bo; Cheng, Shifeng; Kariba, Robert; Muthemba, Samuel; Hendre, Prasad S.; Mayes, Sean; Ho, Wai Kuan; Yssel, Anna; Kendabie, Presidor; Wang, Sibo; Li, Linzhou; Muchugi, Alice; Jamnadass, Ramni; Lu, Haorong; Peng, Shufeng; Deynze, Allen Van; Simons, A. J.; Yana-Shapiro, Howard; Peer, Yves Van de; Xu, Xun; Yang, Huanming; Wang, Jian; Liu, Xin

doi:10.1093/gigascience/giy152

Cited by 122 publications

(112 citation statements)

References 78 publications

(81 reference statements)

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“…We have shown that nanopore DRS has the potential to refine multiple features of Arabidopsis genome annotation and to generate the clearest map to date of m 6 A locations, despite the genome sequence being available since 2000 44 . Modern agriculture is dominated by a handful of intensely researched crops 45 , but to diversify global food supply, enhance agricultural productivity and tackle malnutrition there is a need to focus on crops utilized in rural societies that have received little attention for crop improvement 46 . Based on our experience with Arabidopsis, we anticipate that the combination of nanopore DRS and other sequencing approaches will improve genome annotation.…”

Section: Discussionmentioning

confidence: 99%

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

Parker

Knop

Sherwood

et al. 2019

Preprint

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21Understanding genome organization and gene regulation requires insight into RNA transcription, 22 processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a 23 wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA 24 methylation (m 6 A). Here we show that m 6 A can be mapped in full-length mRNAs transcriptome-wide 25 and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, 26 poly(A) site choice and poly(A) tail length. Loss of m 6 A from 3' untranslated regions is associated 27 with decreased relative transcript abundance and defective RNA 3′ end formation. A functional 28 consequence of disrupted m 6 A is a lengthening of the circadian period. We conclude that nanopore 29 direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length 30 single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying 31 this approach to less well-studied species could transform our understanding of what their genomes 32 encode. 33 34 misidentification of 3′ ends through internal priming 3 , spurious antisense and splicing events 46 produced by RT template switching 4,5 , and the inability to detect all base modifications in the 47 copying process 6 . The fragmentation of RNA prior to short-read sequencing makes it difficult to 48 interpret the combination of authentic RNA processing events and remains an unsolved problem 7 . 49We investigated whether long-read direct RNA sequencing (DRS) with nanopores 8 could 50 reveal the complexity of Arabidopsis mRNA processing and modifications. In nanopore DRS, the 51 protein pore (nanopore) sits in a membrane through which an electrical current is passed, and intact 52 RNA is fed through the nanopore by a motor protein 8 . Each RNA sequence within the nanopore 53 (5 bases) can be identified by the magnitude of signal it produces. Arabidopsis is a pathfinder model 54 in plant biology, and its genome annotation strongly influences the annotation and our 55 understanding of what other plant genomes encode. We applied nanopore DRS and Illumina RNAseq 56 to wild-type Arabidopsis (Col-0) and mutants defective in m 6 A 9 and exosome-mediated RNA decay 10 . 57We reveal m 6 A and combinations of RNA processing events (alternative patterns of 5′ capped 58 transcription start sites, splicing, 3′ polyadenylation and poly(A) tail length) in full-length Arabidopsis 59 mRNAs transcriptome-wide. 60 61 Results 62Nanopore DRS detects long, complex mRNAs and short, structured non-coding RNAs 63We purified poly (A)+ RNA from four biological replicates of 14-day-old Arabidopsis Col-0 seedlings. 64We incorporated synthetic External RNA Controls Consortium (ERCC) RNA Spike-In mixes into all 65 replicates 11,12 and carried out nanopore DRS. Illumina RNAseq was performed in parallel on similar 66 material. Using Guppy base-calling (Oxford Nanopore Technologies) and minimap2 alignment 67 software 13 , we identified around 1 mi...

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Section: Discussionmentioning

confidence: 99%

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

Parker

Knop

Sherwood

et al. 2019

Preprint

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“…], rice [ Oryza sativa L.], soybean [ Glycine max (L.) Merr. ], and tomato [ Solanum lycopersicum L.]), and the fifth is an underutilized legume with a recently sequenced genome (lablab, Lablab purpureus (L.) Sweet; Fabaceae; Chang et al., ). The species span a range of genome sizes (157–1078 Mbp/1C).…”

Section: Methodsmentioning

confidence: 99%

“…This increases the efficiency of SSR identification in non-model species; however, transferability in different groups of species is likely to be variable. Chang et al, 2018). The species span a range of genome sizes (157-1078 Mbp/1C).…”

mentioning

confidence: 99%

Optimizing depth and type of high‐throughput sequencing data for microsatellite discovery

Chapman

2019

Appl Plant Sci

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PremiseSimple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discovery, has not been tested.MethodsI used genome and transcriptome high‐throughput sequencing data at a range of sequencing depths to compare efficacy of SSR identification. I then tested primers from tomato for amplification, polymorphism, and transferability to related species.ResultsSmall assemblies (two million read pairs) identified ca. 200–2000 potential markers from the genome assemblies and ca. 600–3650 from the transcriptome assemblies. Genome‐derived contigs were often short, potentially precluding primer design. Genomic SSR primers were less transferable across species but exhibited greater variation (partially explained by being composed of more repeat units) than transcriptome‐derived primers.DiscussionSmall high‐throughput sequencing resources may be sufficient for identification of hundreds of SSRs. Genomic data may be preferable in species with low polymorphism, but transcriptome data may result in longer loci (more amenable to primer design) and primers may be more transferable to related species.

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“…This study is part of the African Orphan Crops Consortium (AOCC), an international public-private partnership. A goal of this global initiative is to sequence, assemble and annotate the genomes of 101 traditional African food crops by 2020 [22,23]. Both breadfruit and jackfruit are nutritious [24][25][26][27] and have potential to increase food security, especially in tropical areas.…”

Section: Introductionmentioning

confidence: 99%

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Sahu¹,

Liu²,

Yssel

et al. 2019

Preprint

Self Cite

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Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 100 pounds). To date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2,822 and 2,034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch-and sucrose metabolism, photosynthesis and others. The copy number of several starch synthesis related genes were found increased in jackfruit and breadfruit compared to closely related species, and the tissue specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

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The draft genomes of five agriculturally important African orphan crops

Cited by 122 publications

References 78 publications

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

Optimizing depth and type of high‐throughput sequencing data for microsatellite discovery

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

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