The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

Guardo, Mario Di; Moretto, Marco; Moser, Mirko; Catalano, C.; Troggio, Michela; Deng, Zhiming; Cestaro, Alessandro; Caruso, Marco; Distefano, Gaetano; Malfa, Stefano La; Bianco, Luca; Gentile, Alessandra

doi:10.1007/s11295-021-01528-5

Cited by 17 publications

(18 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, we compared two haplotype gap-free assemblies with published haplotype assemblies ( C. limon [L.] Burm. f. genome v1.0) [ 15 ]. The BUSCO completeness of the two haplotype gap-free assemblies was 98.6%, which was higher than values for C. limon [L.] Burm f. genome v1.0-primary and C. limon [L.] Burm f. genome v1.0-alternative (the previous assembly) by 2.7 and 3.8%, respectively.…”

Section: Resultsmentioning

confidence: 99%

A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance

Bao

Ziyan

Yao

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

The lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruit worldwide. Lemon also tolerates Huanglongbing disease, which is a devastating citrus disease. Here, we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps. While a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5 %), 147.4 Mb from mandarin (23.3 %), and 147.1 Mb from pummelo (23.2 %). The genome included 30,528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant-pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG) / Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that the phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.

show abstract

Section: Resultsmentioning

confidence: 99%

A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance

Bao

Ziyan

Yao

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

show abstract

“…Genome assembly completeness was assessed using Benchmarking Universal Single-Copy Orthologs against 425 single copy orthologs in viridiplantae lineage (BUSCO v5.2.2) [38] and the contiguity was assessed using QUAST (version 5.0.2) [39]. The longest nine scaffolds were assigned to chromosomes that correspond with previously published chromosome-scale genomes; C. sinensis v.03 [40], C. maxima [41] and C. limon [14]. The synteny among the genomes were visualized with D-Genies v.1.4 [42].…”

Section: Methodsmentioning

confidence: 99%

Haplotype resolved chromosome level genome assembly ofCitrus australisreveals disease resistance and other citrus specific genes

Nakandala

Masouleh

Smith³

et al. 2022

Preprint

View full text Add to dashboard Cite

Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus. Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased, with the available genomes of varying accuracy and completeness. We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species; Citrus australis (round lime) using highly accurate PacBio HiFi long reads, complemented with Hi-C scaffolding. Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C. australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness (BUSCO). Repeat analysis showed that more than 50% of the genome contained interspersed repeats. Among them, LTR elements were the predominant type (21.0%), of which LTR Gypsy (9.8 %) and LTR copia (7.7 %) elements were the most abundant repeats. A total of 29,464 genes and 32,009 transcripts were identified in the genome. Of these, 28,222 CDS (25,753 genes) had BLAST hits and 21,401 CDS (75.8%) were annotated with at least one GO term. Citrus specific genes for antimicrobial peptides, defense, volatile compounds and acidity regulation were identified. This chromosome scale, and haplotype resolved C. australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.

show abstract

“…This is also suggested based on the large number of unigenes, 408 in B. rotunda, notably more than twice that of Ensete glaucum [57], and 46,765 duplicated genes (65.8% of the B. rotunda genome, with at least 50% support). As noted in Citrus limon [65], high levels of heterozygosity complicate the assembly process and due to the clonal propagation nature of the fingerroot ginger, offspring resulting from sexual hybridization is rather limited. Thus, we applied a similar approach as reported by Chin et al (2016) and Baek et al (2018), for the assembly of the B. rotunda genome [66,67].…”

Section: Discussionmentioning

confidence: 99%

Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)

Taheri

Teo

Heslop-Harrison

et al. 2022

IJMS

View full text Add to dashboard Cite

Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.

show abstract

The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

Cited by 17 publications

References 48 publications

A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance

A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance

Haplotype resolved chromosome level genome assembly ofCitrus australisreveals disease resistance and other citrus specific genes

Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)

Contact Info

Product

Resources

About