Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers
Abstract
Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.
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BibTeX
@misc{charlotte2026chromosomescale,
title = {{Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers}},
author = {Cravero Charlotte and Lesur-Kupin Isabelle and Choisne Nathalie and Leple Jean-Charles and Vassilieff Helena and de Miguel Marina and Gautier Véronique and Belmonte Elodie and Pailler Vincent and Poncet Charles and Dia Sow Mamadou and Huneau Cecile and Klopp Christophe and Ehrenmann Francois and Giovanni Vendramin and Alía Ricardo and Bellec Arnaud and Panaud Olivier and Maumus Florian and Salse Jérôme and Pichot Christian and Plomion Christophe and William William Marande},
howpublished = {HAL},
year = {2026},
month = jul,
doi = {10.64898/2026.07.23.736688},
url = {https://hal.science/hal-05746353v1},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers
AU - Cravero Charlotte
AU - Lesur-Kupin Isabelle
AU - Choisne Nathalie
AU - Leple Jean-Charles
AU - Vassilieff Helena
AU - de Miguel Marina
AU - Gautier Véronique
AU - Belmonte Elodie
AU - Pailler Vincent
AU - Poncet Charles
AU - Dia Sow Mamadou
AU - Huneau Cecile
AU - Klopp Christophe
AU - Ehrenmann Francois
AU - Giovanni Vendramin
AU - Alía Ricardo
AU - Bellec Arnaud
AU - Panaud Olivier
AU - Maumus Florian
AU - Salse Jérôme
AU - Pichot Christian
AU - Plomion Christophe
AU - William William Marande
PY - 2026
DA - 2026/07/24
PB - HAL
DO - 10.64898/2026.07.23.736688
UR - https://hal.science/hal-05746353v1
AB - Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.
ER -