Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness

Abstract

Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of approximately 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant-pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat (NBS-LRR) gene family, which may be linked to the defense response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.

Haplotype‐resolved genome assembly provides insights into the evolution of S‐locus supergene in distylous Nymphoides indica

“…S7). This result is consistent with earlier work, which proposed that N. indica experienced a recent WGD (S. Yang et al, 2022). The Ks distribution for two gene pairs was c. 2.52 (Nin-hap117766 and NinKHZ2), and c. 3.1 (Ninhap113470 and NinBAS1), respectively (Fig.…”

“…S7). This result is consistent with earlier work, which proposed that N. indica experienced a recent WGD (S. Yang et al ., 2022). The Ks distribution for two gene pairs was c .…”

“…For the GWAS analyses, we collected young leaves from 13 and 15 individuals of the L‐ and S‐morphs, respectively, and conducted DNA extraction, library preparation, and whole‐genome resequencing following protocols detailed in Yang et al . (2022). We sequenced each sample to an expected coverage of 10×.…”

“…For the genome assembly of the S‐morph plant, we used H ifiasm v.0.16.0 (Cheng et al ., 2021) to assemble the PacBio HiFi reads into a haplotype‐resolved genome and a haploid genome. The Hi‐C data of the same individual, which was generated in our previous study (Yang et al ., 2022), were retrieved from CNCB (CNP0002767). We first mapped the clean Hi‐C reads to the haploid assembly to construct chromosome‐level assemblies using J uicer (Durand et al ., 2016b) and built primary scaffolds with the 3D‐DNA pipeline (Dudchenko et al ., 2017).…”

“…We predicted protein‐coding genes by combining de novo , homology‐based, and transcriptome‐based approaches according to methods detailed in our previous study of N. indica (Yang et al ., 2022). We mapped all consensus gene models to public databases, including Swiss‐Prot and NR, using B lastp (Camacho et al ., 2009) searches with an e‐value cutoff of 1e‐5 and aligned to the egg NOG database v.5.0 (Huerta‐Cepas et al ., 2019) using egg NOG‐mapper v.2 (Cantalapiedra et al ., 2021).…”