Chromosome‐level reference genome of the soursop (<i>Annona</i><i>muricata</i>): A new resource for Magnoliid research and tropical pomology

Strijk, Joeri S.; Hinsinger, Damien Daniel; Roeder, Mareike; Chatrou, Lars W.; Couvreur, Thomas L.P.; Erkens, Roy; Sauquet, Hervé; Pirie, Michael D.; Thomas, Daniel C.; Cao, Kaihua

doi:10.1111/1755-0998.13353

Cited by 20 publications

(21 citation statements)

References 70 publications

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“…For the second genomic DNA sequencing approach, the sequencing library was prepared using the SMRTbell Express Template The third genomic DNA sequencing approach was the generation of a Hi-C library, as recently described (Strijk et al, 2021). Briefly, the steps were as follows: (1) DNA cross-linking, (2) MboI digestion,…”

Section: Dna Sequencing and Quality Controlmentioning

confidence: 99%

A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)

Liu

Mei

et al. 2022

Molecular Ecology Resources

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There are approximately 450 species of oaks (Quercus L., Fagaceae) and they are the dominant tree species in many ecosystems and landscapes throughout the Northern Hemisphere (Plomion et al., 2016).Classifying oak trees is challenging because of the existence of a large number of interspecific morphological characteristics and intraspecific morphological variations, partly due to hybridization and introgression, subsequently influencing the phylogenetic reconstruction of oak spe-

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Section: Dna Sequencing and Quality Controlmentioning

confidence: 99%

A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)

Liu

Mei

et al. 2022

Molecular Ecology Resources

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“…The assembly statistics of this study showed a higher number of assembled transcripts and unigenes compared to other Annonaceae transcriptomes [ 19 , 20 , 21 ]. Recently, the first soursop genome was assembled at a chromosome level from PacBio and Illumina short-reads, identifying 23,375 protein-coding genes using de novo RNA-seq and homology searches [ 22 ]. In this study, similar results were obtained, finding 21,494 ORF from 95,832 unigenes under different postharvest storage conditions.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Soursop (Annona muricata L.) Fruit under Postharvest Storage Identifies Genes Families Involved in Ripening

Palomino-Hermosillo

Berúmen-Varela

Ochoa-Jiménez

et al. 2022

Plants

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Soursop (Annona muricata L.) is climacteric fruit with a short ripening period and postharvest shelf life, leading to a rapid softening. In this study, transcriptome analysis of soursop fruits was performed to identify key gene families involved in ripening under postharvest storage conditions (Day 0, Day 3 stored at 28 ± 2 °C, Day 6 at 28 ± 2 °C, Day 3 at 15 ± 2 °C, Day 6 at 15 ± 2 °C, Day 9 at 15 ± 2 °C). The transcriptome analysis showed 224,074 transcripts assembled clustering into 95, 832 unigenes, of which 21, 494 had ORF. RNA-seq analysis showed the highest number of differentially expressed genes on Day 9 at 15 ± 2 °C with 9291 genes (4772 up-regulated and 4519 down-regulated), recording the highest logarithmic fold change in pectin-related genes. Enrichment analysis presented significantly represented GO terms and KEGG pathways associated with molecular function, metabolic process, catalytic activity, biological process terms, as well as biosynthesis of secondary metabolites, plant hormone signal, starch, and sucrose metabolism, plant–pathogen interaction, plant–hormone signal transduction, and MAPK-signaling pathways, among others. Network analysis revealed that pectinesterase genes directly regulate the loss of firmness in fruits stored at 15 ± 2 °C.

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“…Although the impact of new sequencing technologies is certainly evident, it has not been possible to assemble a gap-free genome from telomere to telomere only by shortread sequencing. In more recent genome sequencing projects with high-quality published genomes [36][37][38][39][40][41], the scaffolding of long-read assemblies was complemented with high-throughput long-range data, such as optical maps (BioNano Genomics, San Diego, CA, USA [42,43]), chromosomal conformation sequencing (Hi-C with in vivo fixation of chromosomes [44,45]), or linked-reads sequencing (10× Genomics, 10× Genomics, Inc., Pleasanton, US [46]). Long-range mapping data and long-read sequencing allow haplotype/subgenome-phasing of several tree genomes [47][48][49], solving, to a certain extent, challenges in the complete assembly of highly heterozygous and complex genomes.…”

Section: Approaches For Sequencing Of the Large And Heterozygous Tree...mentioning

confidence: 99%

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

Cao

Gailing

2022

IJMS

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Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.

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Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 20 publications

References 70 publications

A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)

A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)

Transcriptome Analysis of Soursop (Annona muricata L.) Fruit under Postharvest Storage Identifies Genes Families Involved in Ripening

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

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