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

Abstract

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.

Telomere Length in Plants Estimated with Long Read Sequencing

“…Inodorus (Wei et al ., 2023) ), Mangifera indica ‘Irwin’ (Henry et al preprint), Musa acuminata Wild type (Liu et al ., 2023) and Cavendish (Huang et al ., 2023), Oryza sativa ZS97RS3 and MH63RS3 (Song et al ., 2021), Mycrica rubra (Zhang et al ., 2024) (Supplemental Table S1). However, assembled telomere sequence is often used as a means to an end in confirming a complete assembly; their details are often relegated to supplemental materials or in many cases not clearly reported at all (Belser et al ., 2021; Bao et al ., 2023; He et al ., 2023; Sato et al ., 2023; Sun et al ., 2023; Wang et al ., 2023; Bi et al ., 2024; Z. Wang et al ., 2024).…”

CentIER: accurate centromere identification for plant genomes with sequence specificity information

“…A. chinensis (Han et al, 2023), http://182.92.183.62/; C. limon (Bao et al, 2023), https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=GWHCBFQ00000000.1; E. rufpilus (Wang et al, 2023), http://sugarcane.zhangjisenlab.cn/SugarcaneDB/#/downloads; O. sativa (Song et al, 2021), http://rice.hzau.edu.cn/cgi-bin/rice_rs3/download_ext; V. vinifera (Shi et al, 2023), https://zenodo.org/record/7751391#.ZBgVmcJBy3A; Z. mays (Chen et al, 2023), https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA751841.…”

The Genomes of Australian Wild Limes

“…Recent advances in genomic sequencing technologies have led to the development of chromosome-level genomes for some Citrus species, including C. sinensis (Gao et al 2023; Wang et al 2021), C. limon (Bao et al 2023), C. maxima (Zheng et al 2023) and relatives of Citrus such as Poncirus trifoliata (Peng et al 2020), Murraya paniculata (Yang et al 2023) and Atalantia buxifolia (Yuan et al 2019). High-quality, gap free genomes for Citrus have been developed using Paci c Biosciences circular consensus sequencing (CCS), high-throughput chromatin capture (Hi-C), and Oxford Nanopore Technology (ONT), which have led to the identi cation of candidate genes associated with important characteristics in Citrus (Bao et al 2023). High-quality reference genomes and chromosome-level annotation data are available for two of the Australian Citrus species, C. australis, and C. australasica (Nakandala et al 2023a;2023c).…”