The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

Shi, Tao; Huneau, Cécile; Zhang, Yue; Li, Yan; Chen, Jinming; Salse, Jérôme; Wang, Qingfeng

doi:10.1038/s41477-022-01187-x

Cited by 25 publications

(21 citation statements)

References 97 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the syntenic analysis, the 4:1 collinear relationship between N. fruticans and A. trichopoda suggested that N. fruticans experienced two rounds of WGD events after its divergence from A. trichopoda (Figure 1E). The 4:2 collinear relationship between N. fruticans and the monocot basal species Acorus tatarinowii (Shi et al, 2022) (Figure 1E) and the 4:4 collinear relationship between N. fruticans and the Poales species Ananas comosus (Ming et al, 2015) also supported this inference (Figure S6). The two peaks in the K s distribution also indicated that N. fruticans underwent two WGD events in its evolutionary history.…”

Section: Resultsmentioning

confidence: 58%

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Wu,

Feng,

Wang

et al. 2024

JIPB

View full text Add to dashboard Cite

Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long‐term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome‐level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole‐genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine‐labelled 1 (EM1) and EM6 in N. fruticans underly its crypto‐vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long‐term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

show abstract

Section: Resultsmentioning

confidence: 58%

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Wu,

Feng,

Wang

et al. 2024

JIPB

View full text Add to dashboard Cite

show abstract

“…The deduced SpAMT protein sequences demonstrate most close phylogenetic relationship to their counterparts from S. intermedia , followed by taro, Colocasia esculenta [ 87 ], a plant species which belongs to the group of early-branching monocotyledonous family Araceae [ 88 ], a sister family to Lemnaceae [ 46 ]. The SpAMT proteins also demonstrate significant levels of similarity to the homologues from other monocotyledonous banana, cocos, oil palm, rice and wheat, as well as dicotyledonous Arabidopsis ( Figure 2 ), stressing strong evolutionary conservation of this important protein family along the plants [ 83 , 89 ].…”

Section: Discussionmentioning

confidence: 99%

Ammonium Uptake, Mediated by Ammonium Transporters, Mitigates Manganese Toxicity in Duckweed, Spirodela polyrhiza

Kishchenko

Stepanenko

Straub

et al. 2023

Plants

View full text Add to dashboard Cite

Nitrogen is an essential nutrient that affects all aspects of the growth, development and metabolic responses of plants. Here we investigated the influence of the two major sources of inorganic nitrogen, nitrate and ammonium, on the toxicity caused by excess of Mn in great duckweed, Spirodela polyrhiza. The revealed alleviating effect of ammonium on Mn-mediated toxicity, was complemented by detailed molecular, biochemical and evolutionary characterization of the species ammonium transporters (AMTs). Four genes encoding AMTs in S. polyrhiza, were classified as SpAMT1;1, SpAMT1;2, SpAMT1;3 and SpAMT2. Functional testing of the expressed proteins in yeast and Xenopus oocytes clearly demonstrated activity of SpAMT1;1 and SpAMT1;3 in transporting ammonium. Transcripts of all SpAMT genes were detected in duckweed fronds grown in cultivation medium, containing a physiological or 50-fold elevated concentration of Mn at the background of nitrogen or a mixture of nitrate and ammonium. Each gene demonstrated an individual expression pattern, revealed by RT-qPCR. Revealing the mitigating effect of ammonium uptake on manganese toxicity in aquatic duckweed S. polyrhiza, the study presents a comprehensive analysis of the transporters involved in the uptake of ammonium, shedding a new light on the interactions between the mechanisms of heavy metal toxicity and the regulation of the plant nitrogen metabolism.

show abstract

“…Ancestral genomes are inferred from (see the Materials and methods section) conserved genes (Step 1), orthologous relationships (Step 2), SBs (Step 3) and CARs (Step 4), to provide the best scenario explaining the transition between ancestral and modern genomes. Types of tabular files derived from each step are illustrated at the right to help readers to properly follow the procedure (described in and adapted from ( 20 )).…”

Section: Methodsmentioning

confidence: 99%

SyntenyViewer: a comparative genomics-driven translational research tool

et al. 2023

Self Cite

View full text Add to dashboard Cite

SyntenyViewer is a public web-based tool relying on a relational database available at https://urgi.versailles.inrae.fr/synteny delivering comparative genomics data and associated reservoir of conserved genes between angiosperm species for both fundamental (evolutionary studies) and applied (translational research) applications. SyntenyViewer is made available for (i) providing comparative genomics data for seven major botanical families of flowering plants, (ii) delivering a robust catalog of 103 465 conserved genes between 44 species and inferred ancestral genomes, (iii) allowing us to investigate the evolutionary fate of ancestral genes and genomic regions in modern species through duplications, inversions, deletions, fusions, fissions and translocations, (iv) use as a tool to conduct translational research of key trait-related genes from model species to crops and (v) offering to host any comparative genomics data following simplified procedures and formats Database URL https://urgi.versailles.inrae.fr/synteny

show abstract

The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

Cited by 25 publications

References 97 publications

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Ammonium Uptake, Mediated by Ammonium Transporters, Mitigates Manganese Toxicity in Duckweed, Spirodela polyrhiza

SyntenyViewer: a comparative genomics-driven translational research tool

Contact Info

Product

Resources

About