A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F25%3A00618158" target="_blank" >RIV/61389030:_____/25:00618158 - isvavai.cz</a>

Alternative codes found

RIV/67985939:_____/25:00618158

Result on the web

<a href="https://doi.org/10.1002/tpg2.70010" target="_blank" >https://doi.org/10.1002/tpg2.70010</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/tpg2.70010" target="_blank" >10.1002/tpg2.70010</a>

Result language

angličtina

Original language name

A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium

Original language description

The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa (Chenopodium quinoa Willd.) have served as domesticated staple crops for centuries. Wild Chenopodium species exhibit diverse niche adaptations and are important genetic reservoirs for beneficial agronomic traits, including disease resistance and climate hardiness. To harness the potential of the wild taxa for crop improvement, we developed a Chenopodium pangenome through the assembly and comparative analyses of 12 Chenopodium species that encompass the eight known genome types (A-H). Six of the species are new chromosome-scale assemblies, and many are polyploids, thus, a total of 20 genomes were included in the pangenome analyses. We show that the genomes vary dramatically in size with the D genome being the smallest (similar to 370 Mb) and the B genome being the largest (similar to 700 Mb) and that genome size was correlated with independent expansions of the Copia and Gypsy LTR retrotransposon families, suggesting that transposable elements have played a critical role in the evolution of the Chenopodium genomes. We annotated a total of 33,457 pan-Chenopodium gene families, of which similar to 65% were classified as shell (2% private). Phylogenetic analysis clarified the evolutionary relationships among the genome lineages, notably resolving the taxonomic placement of the F genome while highlighting the uniqueness of the A genome in the Western Hemisphere. These genomic resources are particularly important for understanding the secondary and tertiary gene pools available for the improvement of the domesticated chenopods while furthering our understanding of the evolution and complexity within the genus.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10611 - Plant sciences, botany

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Plant Genome

ISSN

1940-3372

e-ISSN

1940-3372

Volume of the periodical

18

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

28

Pages from-to

e70010

UT code for WoS article

001438210500001

EID of the result in the Scopus database

2-s2.0-85219599365