A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)

Uncovering the Secrets of How Plants Adapt to Water Stress

The frequency of flooding and other naturally occurring stresses caused by global climate change is increasing rapidly worldwide. Recent research has uncovered the morphological, physiological, and molecular mechanisms underlying water stress adaptation in model plants. This review synthesizes recent advances in understanding water adaptation, not only in model terrestrial plants but also in amphibious and aquatic plants. Plants respond to flooding stress through various adaptive strategies, including (1) the low-oxygen quiescence strategy (LOQS), which conserves energy by pausing metabolism and growth during flooding, and (2) the low-oxygen escape strategy (LOES), where plants elongate organs rapidly to reach the water surface and access more oxygen. In amphibious plants, heterophylly enables the production of dramatically different leaf forms to adapt to terrestrial versus submerged environments, representing a third strategy- the "variation" strategy for water stress adaptation. Unlike terrestrial crops, which must "wait" or "escape" during flooding, amphibious plants can naturally thrive in both aquatic and terrestrial habitats. In addition to heterophylly, other mechanisms of water stress adaptation in amphibious and aquatic plants are also discussed. Understanding these mechanisms can advance our knowledge for developing future flood-resilient crops, which are essential for sustainable agriculture under changing climates.

The chromosome-level genome of water hyacinth (Eichhornia crassipes)

OBJECTIVES

Water hyacinth (Eichhornia crassipes) is one of the most notorious invasive aquatic plants in the world and is known to cause significant ecological and socioeconomic impacts. Here, we reported a high-quality chromosome-level genome for water hyacinth, which will be a valuable reference for future investigations of its invasion.

DATA DESCRIPTION

A chromosome-level genome for water hyacinth was constructed by combing MGI short-reads sequencing, PacBio HiFi (High-fidelity) sequencing, and Hi-C sequencing, which resulted in ca. 1132.2 Mb in size the contig and scaffold N50 length of 18.76 Mb and 69.84 Mb, respectively. A total of 1024.36 Mb (90.47%) of the assembled sequences were anchored to 16 pseudochromosomes, dividing into subgenome A (468.72 Mb in size) and subgenome B (555.64 Mb in size). A total of 57,683 protein-coding genes were predicted, including 25,445 protein-coding genes for subgenome A and 27,992 protein-coding genes for subgenome B. Furthermore, the LAI and QV scores of the water hyacinth genome were 12.32 and 48.91, respectively.

The genomic secrets of invasive plants

Genomics has revolutionised the study of invasive species, allowing evolutionary biologists to dissect mechanisms of invasion in unprecedented detail. Botanical research has played an important role in these advances, driving much of what we currently know about key determinants of invasion success (e.g. hybridisation, whole-genome duplication). Despite this, a comprehensive review of plant invasion genomics has been lacking. Here, we aim to address this gap, highlighting recent discoveries that have helped progress the field. For example, by leveraging genomics in natural and experimental populations, botanical research has confirmed the importance of large-effect standing variation during adaptation in invasive species. Further, genomic investigations of plants are increasingly revealing that large structural variants, as well as genetic changes induced by whole-genome duplication such as genomic redundancy or the breakdown of dosage-sensitive reproductive barriers, can play an important role during adaptive evolution of invaders. However, numerous questions remain, including when chromosomal inversions might help or hinder invasions, whether adaptive gene reuse is common during invasions, and whether epigenetically induced mutations can underpin the adaptive evolution of plasticity in invasive populations. We conclude by highlighting these and other outstanding questions that genomic studies of invasive plants are poised to help answer.

Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colours

Pontederia cordata L. is an aquatic ornamental plant native to the Americas but has been widely distributed in South Asia, Australia, and Europe. The genetic mechanisms behind its rapid adaptation and spread have not yet been well understood. To understand the mechanisms for its rapid adaptation, this study assembled the first chromosome-level genome of P. cordata. The genome assembly, which spans 527.5 Mb, is anchored on 8 pseudochromosomes with a scaffold N50 of 48 Mb and encompasses 29,389 protein-coding genes. Further analyses revealed that P. cordata had experienced 3 whole-genome duplications (WGDs) events. These WGDs are associated with gene family expansion and increased numbers of resistance gene analogs and transcription factors. Positive selection analysis indicated that genes derived from tandem duplication (TD) and proximal duplication were more likely to undergo positive selection, and were enriched in plant defense and disease resistance. These results implied that WGDs, TD, and positive selection enhanced the environmental adaptability of P. cordata. In addition, we found that down-regulation of F3'5'H, DFR, ANS, and UFGT likely caused the flower colour variation for P. cordata from violet to white. The first chromosome-level genome of P. cordata here provides a valuable genomic resource for investigating the rapid adaptation and flower colour variation of the species.

The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery

Heteranthery, the occurrence of functionally and structurally distinct stamens within a flower, represents a striking example of convergent evolution among diverse animal-pollinated lineages. Although the ecological basis of this somatic polymorphism is understood, the developmental and molecular mechanisms are largely unknown. To address this knowledge gap, we selected Monochoria elata (Pontederiaceae) as our study system due to its typical heterantherous floral structure. We constructed a chromosome-level genome assembly of M. elata, conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery. We focused on three key stamen characteristics-colour, spatial patterning, and filament elongation-selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species. Our analyses suggest that gene networks involving MelLEAFY3, MADS-box, and TCP genes regulate stamen identity, with anthocyanin influencing colour, and lignin contributing to filament elongation. Additionally, variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence. Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.

A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)

Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.