A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)

Abstract

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time of Cladopus chinensis (106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged species. Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses, including WUSCHEL (WUS), ASYMMETRIC LEAVES (ASL), SHOOT MERISTEMLESS (STM), NAC2, NAC8, NAC29, NAC47, NAC73, NAC83 and NAC102. These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.

Insights into amphicarpy from the compact genome of the legume Amphicarpaea edgeworthii

“…Serine/threonine protein kinases are involved in the response to environmental stresses (such as high salt, drought, and low temperature) that regulate multiple life processes in cells. It has been speculated that the contraction of these types of gene families affect the accumulation of secondary metabolites and reduces environmental adaptability, resulting in the survival of Cladopus chinensis only in good‐quality water (Xue et al ., 2020). Similarly, A. edgeworthii is sensitive to various environmental stresses and is difficult to cultivate in the greenhouse.…”

De novo assembly of a new Olea europaea genome accession using nanopore sequencing

“…Olive has high heterozygosity, high numbers of repetitive sequences, and a large genome, which has hindered the production of a high-quality reference assembly of the two versions of the olive genome. Technological improvements have increased the yield and length of genome sequencing, particularly third-generation sequence technologies, such as PacBio third-generation sequencing and Oxford Nanopore third-generation sequencing (ONT) technology 8 , 9 . In addition, a genome-wide chromosome conformation capture technique, Hi-C, is often used to further assemble chromosome-scale genomes based on a sequenced draft genome 10 .…”

Chitosan Oligosaccharide Production Potential of Mitsuaria sp. C4 and Its Whole-Genome Sequencing

“…PCR amplification of the 16S rRNA gene was carried out by using procedures described by Wei et al (2021) . Molecular phylogenetic analysis was performed by using MEGA7 software via the maximum likelihood method ( Xue et al, 2020 ).…”

“…Approximately 1.70- and 1.74-Gb clean data were generated by PacBio and Illumina, respectively. The data were corrected, trimmed, and assembled using CANU (version 1.6) with the parameters corOutCoverage = 80 and corMinCoverage = 0, then further polished by the Pilon programs with default parameters ( Xue et al, 2020 ). The completeness of the C4 genome was assessed with BUSCO ( Simão et al, 2015 ).…”

“…1 Non-coding RNA and small RNAs were predicted by alignment to the Rfam and miRNA databases using tRNAsan-SE and BLASTN, respectively ( Liu et al, 2020 ). Functional annotation of the protein-coding genes in the EggNOG, Gene Ontology (GO), Clusters of Orthologous Genes (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and carbohydrate-active enzyme (CAZy) databases was performed using BLASTP software ( Lombard et al, 2014 ; Xue et al, 2020 ). CAZy can be classified into five classes, including glycoside decomposing enzymes (GHs), glycosyltransferases (GTs), polysaccharide lyases (PLs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), and oxidoreductases (AAs) ( Park et al, 2018 ).…”