Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

Abstract

Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid herbaceous plant with 26 chromosomes (2n = 26) and belongs to the family Cucurbitaceae. To address the limited knowledge of the genome of Luffa species, the chromosome‐level genome of L. cylindrica was assembled and analysed using PacBio long reads and Hi‐C data. We combined Hi‐C data with a draft genome assembly to generate chromosome‐length scaffolds. Thirteen scaffolds corresponding to the 13 chromosomes were assembled from 1,156 contigs to a final size of 669 Mb with a contig N50 size of 5 Mb and a scaffold N50 size of 53 Mb. After removing redundant sequences, 416.31 Mb (62.18% of the genome) of repeat sequences was detected. Subsequently, 31,661 protein‐coding genes with an average of 5.69 exons per gene were identified in the L. cylindrica genome using de novo methods, transcriptome data and homologue‐based approaches. In addition, 27,552 protein‐coding genes (87.02%) were annotated in five databases. According to the phylogenetic analysis, L. cylindrica is closely related to Cucurbita and Cucumis species and diverged from their common ancestor ~28.6–67.1 million years ago. Genome collinearity analysis was performed in Cucurbita moschata, Cucumis sativus and L. cylindrica, and it demonstrated a high degree of conserved gene order in these three species. The completeness of the genome will provide high‐quality genomic knowledge on breeding and reveal genetic variation in L. cylindrica.

De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements

“…The numbers of protein‐coding genes in L. acutangula and L. cylindrica obtained for our assemblies were similar to the figure previously reported for L. cylindrica genome (Zhang et al., 2020), while the proportions of repetitive sequences identified in our genome assemblies (62% for L. acutangula and 57% for L. cylindrica ) were slightly lower than the percentage reported for L. cylindrica (73%) in Zhang et al. (2020). The availability of this assembly enabled comparative genomics/phylogenetic studies of the Cucurbitaceae family members.…”

“…De novo assemblies of PacBio sequences from L. acutangula and L. cylindrica yielded draft genomes of 734.6 Mb and 689.8 Mb in 2,280 and 3,570 scaffolds with scaffold N50 of 786,130 (L50 = 220 scaffolds) and 578,616 bases (L50 = 316 scaffolds), respectively (Table 1). Analyses of k ‐mer distribution of the genome sequencing reads provided estimated genome sizes of 760 Mb and 773 Mb for L. acutangula and L. cylindrica , respectively, close to the figure previously reported for L. cylindrica (An et al., 2017; Zhang et al., 2020) (Figure S1). The heterozygosity of L. acutangula and L. cylindrica was 0.41 and 0.25, respectively.…”

“…The sizes of the preliminary assemblies were 96.5% and 89% of the estimated genome sizes in L. acutangula and L. cylindrica , respectively, based on k‐ mer analyses. A previous publication on L. cylindrica genome assembly also reported that the assembly size (669 Mb) was smaller than the estimated genome size (737 Mb) based on k‐ mer analysis (91% of the estimated size) (Zhang et al., 2020). The discrepancy observed between the assembly size and the k ‐mer size estimation could be due to a large number of repetitive sequences (Pflug, Holmes, Burrus, Spencer Johnston, & Maddison, 2020).…”

Sustainable Cucurbit Breeding and Production in Asia Using Public–Private Partnerships by the World Vegetable Center

“…Genomic tools have improved the breeding efficiency of major cucurbit crops, and transgenic and genome-edited plants have been produced [47,48]. The availability of whole genome sequences of C. moschata [49], M. charantia [50], and L. cylindrica [51] is stimulating molecular breeding approaches in these crops. Several markers putatively associated with resistance to ZYMV in pumpkin and CPM in bitter gourd have been proposed and are being validated.…”

De novo chromosome-level genome assembly of Chinese walnut (Juglans cathayensis Dode)

“…Compared to previously available genome assemblies for this species, the Scaffold N50 value was improved 163 fold (contig N50 size of J. cathayensis v2.0 was 23,789,296 bp versus 145,095 bp contig N50 size for J. cathayensis v1.0), and the final calculated genome size is smaller (580Mb, v1.0 versus 548Mb, v2.0) (Figure1; Table S12). Through Hi-C, a chromosome-level genome was obtained with a scaffold size of 36Mb (Table S12) and scaffolds resolved into 16 chromosomes, unlike the previously available genome (J. cathayensis v1.0; Stevens et al, 2018) (Table S5, Table S12) (DeMaere & Darling, 2019;Zhang et al, 2020c;Chen et al, 2020;Choi et al, 2020). We predicted 29,032 protein-coding genes from the generated assembly.…”