ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016
The draft genome of MD-2 pineapple using hybrid error correction of long reads.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- Single-Molecule Real-Time Sequencing for Identifying Sexual-Dimorphism-Related Transcriptomes and Genes in the Chinese Soft-Shelled Turtle (Animals : an open access journal from MDPI · 2023Article
- Identification of bromelain subfamily proteases encoded in the pineapple genome.Scientific reports · 2023Article
- Genome-wide identification and expression profile analysis of SWEET genes in Chinese jujube.PeerJ · 2023Article
- Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus.G3 (Bethesda, Md.) · 2022Article
- Heterologous Expression and Catalytic Properties of Codon-Optimized Small-Sized Bromelain from MD2 Pineapple.Molecules (Basel, Switzerland) · 2022Article
- Comparison of ONT and CCS sequencing technologies on the polyploid genome of a medicinal plant showed that high error rate of ONT reads are not suitable for self-correction.Chinese medicine · 2022Article
- A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae.GigaScience · 2022Article
- Genome assembly, annotation, and comparative analysis of the cattail Typha latifolia.G3 (Bethesda, Md.) · 2022Article
- The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color.G3 (Bethesda, Md.) · 2022Article
- Article
- Soluble Expression and Catalytic Properties of Codon-Optimized Recombinant Bromelain from MD2 Pineapple in Escherichia coli.The protein journal · 2021Article
- Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau.Scientific reports · 2020Article
- Article
- Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.Plant biotechnology journal · 2018Article
- Article
- Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple.Scientific reports · 2017Article
- High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development.Nature genetics · 2017Article
- The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.BMC genomics · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The introduction of the elite pineapple variety, MD-2, has caused a significant market shift in the pineapple industry. Better productivity, overall increased in fruit quality and taste, resilience to chilled storage and resistance to internal browning are among the key advantages of the MD-2 as compared with its previous predecessor, the Smooth Cayenne. Here, we present the genome sequence of the MD-2 pineapple (Ananas comosus (L.) Merr.) by using the hybrid sequencing technology from two highly reputable platforms, i.e. the PacBio long sequencing reads and the accurate Illumina short reads. Our draft genome achieved 99.6% genome coverage with 27,017 predicted protein-coding genes while 45.21% of the genome was identified as repetitive elements. Furthermore, differential expression of ripening RNASeq library of pineapple fruits revealed ethylene-related transcripts, believed to be involved in regulating the process of non-climacteric pineapple fruit ripening. The MD-2 pineapple draft genome serves as an example of how a complex heterozygous genome is amenable to whole genome sequencing by using a hybrid technology that is both economical and accurate. The genome will make genomic applications more feasible as a medium to understand complex biological processes specific to pineapple.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.