Advances in reconstructing the genome of Vanilla planifolia: Addressing partial endoreplication challenges
Despite Vanilla planifolia's economic importance, genomic resources decisive in modern diversity studies and breeding programs have been lacking. Recent attempts to reconstruct this 4.09 Gb diploid genome (16 pairs of chromosomes) revealed insights into gene (~59,000) and repeat content (72% of the genomic sequence). However, none fully succeeded in reconstructing the entire sequence, with the most complete assembly reaching 82% of the expected size and anchoring only one-third of its sequence on a total of 14 pairs of chromosomes, meaning that two pairs are still missing. In addition to frequent aneuploidy and a high rate of repeats, the main cause of the difficulties encountered seems to be partial endoreplication (PE), an orchid specific phenomenon involving several replication rounds of a fraction of the genome without cell division. PE varies in genome proportion and amplification intensity depending on the species and the tissues observed. Latest efforts from the Vaniseq consortium, leveraging tissue selection and technological advancements, are finally leading to a complete and more contiguous assembly, focusing on a better understanding of PE. All in all, this assembly and its refined annotation, along with the recent increase of Vanilla related omics data, should open up new possibilities in several fields, including vanilla varietal improvement and diversity studies.
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | conference_item biblioteca |
| Language: | eng |
| Published: |
CIRAD
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| Online Access: | http://agritrop.cirad.fr/609710/ http://agritrop.cirad.fr/609710/1/Piet_2024_IVC5.pdf |
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| Summary: | Despite Vanilla planifolia's economic importance, genomic resources decisive in modern diversity studies and breeding programs have been lacking. Recent attempts to reconstruct this 4.09 Gb diploid genome (16 pairs of chromosomes) revealed insights into gene (~59,000) and repeat content (72% of the genomic sequence). However, none fully succeeded in reconstructing the entire sequence, with the most complete assembly reaching 82% of the expected size and anchoring only one-third of its sequence on a total of 14 pairs of chromosomes, meaning that two pairs are still missing. In addition to frequent aneuploidy and a high rate of repeats, the main cause of the difficulties encountered seems to be partial endoreplication (PE), an orchid specific phenomenon involving several replication rounds of a fraction of the genome without cell division. PE varies in genome proportion and amplification intensity depending on the species and the tissues observed. Latest efforts from the Vaniseq consortium, leveraging tissue selection and technological advancements, are finally leading to a complete and more contiguous assembly, focusing on a better understanding of PE. All in all, this assembly and its refined annotation, along with the recent increase of Vanilla related omics data, should open up new possibilities in several fields, including vanilla varietal improvement and diversity studies. |
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