A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in <i>Chenopodium</i>
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60460709%3A41330%2F25%3A103593" target="_blank" >RIV/60460709:41330/25:103593 - isvavai.cz</a>
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>
Alternative languages
Result language
angličtina
Original language name
A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in <i>Chenopodium</i>
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
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10611 - Plant sciences, botany
Result continuities
Project
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Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
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
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UT code for WoS article
001438210500001
EID of the result in the Scopus database
2-s2.0-85219599365