Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Hulse‐Kemp, Amanda M.; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa; Jaffe, David B.; Williams, Stephen R.; Weisenfeld, Neil; Ramakrishnan, S.; Kumar, Vijay; Shah, Preyas; Schatz, Michael C.; Church, Deanna M.; Deynze, Allen Van

doi:10.1038/s41438-017-0011-0

Cited by 128 publications

(95 citation statements)

References 36 publications

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“…10X linked-read sequencing provides an alternative way to integrate the advances of shortread and long-fragment sequencning. Novel computational approaches leveraging the special characteristics of 10x Genomics data have already generated significant advances in power and accuracy of haplotyping 35,36 , cancer genome reconstruction 37,38 , metagenome assemblies 39 , and de novo assembly of human and other genomes 14,40,41 , compared to standard Illumina short-fragment sequencing. 10x linked-read sequencing combines low perbase error and good small-variant discovery with long-range information for much improved SV detection in mapping-based approaches 38,42 , and the possibility of long-range contiguity in de novo assembly 40,41,43 .…”

Section: Introductionmentioning

confidence: 99%

De novo diploid genome assembly for genome-wide structural variant detection

Zhang

Zhou

Weng

et al. 2019

Preprint

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Structural variants (SVs) in a personal genome are important but, for all practical purposes, impossible to detect comprehensively by standard short-fragment sequencing. De novo assembly, traditionally used to generate reference genomes, offers an alternative means for variant detection and phasing but has not been applied broadly to human genomes because of fundamental limitations of short-fragment approaches and high cost of long-read technologies. We here show that 10x linked-read sequencing, which has been applied to assemble human diploid genomes into high quality contigs, supports accurate SV detection.We examined variants in six de novo 10x assemblies with diverse experimental parameters from two commonly used human cell lines, NA12878 and NA24385. The assemblies are effective in detecting mid-size SVs, which were discovered by simple pairwise alignment of the assemblies' contigs to the reference (hg38). Our study also shows that the accuracy of SV breakpoint at base-pair level is high, with a majority (80% for deletion and 70% for insertion) of SVs having precisely correct sizes and breakpoints (<2bp difference). Finally, setting the ancestral state of SV loci by comparing to ape orthologs allows inference of the actual molecular mechanism (insertion or deletion) causing the mutation, which in about half of cases is opposite to that of the reference-based call. Interestingly, we uncover 214 SVs that may have been maintained as polymorphisms in the human lineage since before our divergence from chimp. Overall, we show that de novo assembly of 10x linked-read data can achieve cost-effective SV detection for personal genomes.

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Section: Introductionmentioning

confidence: 99%

De novo diploid genome assembly for genome-wide structural variant detection

Zhang

Zhou

Weng

et al. 2019

Preprint

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“…We [47] web platform (https://solgenomics.net/tools/blast/), depending on the databases status. "N.sylvestris Genome", "N.tomentosiformis Genome", "N.tabacum BX Genome", "N.benthamiana v1.0.1", "Tomato ITAG release 3.20", "Potato PGSC DM v3 scaffolds", "Eggplant draft genome (release 2.5.1)" and "Capsicum annuum UCD10X genome chromosomes (v1.0)" databases [34,[48][49][50][51][52] were used, respectively. Arabidopsis AtHAE, AtHSL1 and AtHSL2 protein sequences were retrieved from Phytozome v12.1, TAIR10 database and were used to identify the HAE-like members of the selected Solanaceae species in the same way as described above.…”

Section: Resultsmentioning

confidence: 99%

Differential expression of IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like genes in Nicotiana benthamiana during corolla abscission, stem growth and water stress

Ventimilla

Domingo

Talón

et al. 2019

Preprint

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Background IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like signaling peptides and the associated HAE (HAESA)-like family of receptor kinases were originally reported in the model plant Arabidopsis thaliana (Arabidopsis) to be involved in the regulation of abscission. IDA peptides, as cell-to-cell communication elements, appear to be implicated in many developmental processes that rely on cell separation events, and even in the responses to abiotic stresses. However, the knowledge related to the molecular machinery regulating abscission and other cell separation processes in economically important crops is scarce. In this work, we determined the conservation and phylogeny of the IDA-like and HAE-like gene families in relevant species of the Solanaceae family and analyzed the expression of these genes in Nicotiana benthamiana to identify members involved in abscission, stem growth and response to drought conditions. Results The phylogenetic relationships among the IDA-like members of the species of Solanaceae studied, grouped the NbenIDA1 (A and B) and NbenIDA2 (A and B) pairs of genes with the Arabidopsis prepropeptides related to abscission. In silico analyses of the regulatory elements of the promoter region of IDA-like members showed that these two pairs of genes, NbenIDA1 and NbenIDA2, contained drought and hormonal response elements, although NbenIDA2A lacked the hormonal regulatory elements. Expression analyses showed that both NbenIDA1 genes were upregulated during corolla abscission. NbenIDA1 and NbenIDA2 genes showed tissue differential expression under water stress conditions, since NbenIDA1 genes were highly expressed in stressed leaves while NbenIDA2 genes, especially NbenIDA2B, were highly expressed in stressed roots. In non-stressed active growing plants, nodes and internodes were the tissues with the highest expression levels of all members of the IDA-like family and their putative HAE-like receptors. Conclusion The results suggest that NbenIDA1A and NbenIDA1B are both involved in the natural process of corolla abscission while the NbenIDA1 and NbenIDA2 pair of genes are implicated in the response to water stress. The data also suggest that IDA peptides may be important during stem growth and development. These results add new evidence that the functional module formed by IDA peptides and its receptor kinases, as defined in Arabidopsis, may also be conserved in Solanaceae.

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“…The recent efforts by Kim et al (2017c) and Hulse-Kemp et al (2018) emphasize the need for the continued improvement of the currently available genome resources, as there are inherent shortcomings in each of the used technologies. To move Capsicum genomics forward, a special effort must be directed toward integrating these resources and improving them to ensure that regions of particular interest to breeders, such as disease resistance loci, which are likely to be located in particularly problematic regions of the genome assemblies, are improved and are not omitted from the reference genomes.…”

Section: Capsicum Genomicsmentioning

confidence: 99%

Capsicum—An Abbreviated Compendium

Jarret¹,

Barboza²,

Batista³

et al. 2019

J. Amer. Soc. Hort. Sci.

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Pepper (Capsicum L.) is a major vegetable and spice crop worldwide. Global production of both fresh and dried fruit continues to increase steadily in terms of area harvested and yield. Various topics are addressed in this review, including recent additions to and clarification of Capsicum taxonomy, genetic resources of Capsicum, cytogenetic studies, the current status of our understanding of the mechanisms affecting the biosynthesis of capsaicinoids, the use of gene mutations to elucidate carotenoid biosynthetic pathways and their regulation, and recent advances in whole-genome sequencing and assembly.

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Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Cited by 128 publications

References 36 publications

De novo diploid genome assembly for genome-wide structural variant detection

De novo diploid genome assembly for genome-wide structural variant detection

Differential expression of IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like genes in Nicotiana benthamiana during corolla abscission, stem growth and water stress

Capsicum—An Abbreviated Compendium

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