Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

Cao, Shuai; Sawettalake, Nunchanoke; Shen, Lisha

doi:10.1093/gigascience/giae043

Cited by 4 publications

References 98 publications

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Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

Cao,

Sawettalake,

Shen

2024

GigaScience

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Background Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With a highly complex genome (∼2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands of gaps, impeding a comprehensive understanding of the lettuce genome. Findings Here, we present a near-complete gapless reference genome for cutting lettuce with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem lettuce genome, we identify 127,681 structural variations (SVs, present in 0.41 Gb of sequence), reflecting the divergence of leafy and stem lettuce. Interestingly, these SVs are related to transposons and DNA methylation states. Furthermore, we identify 4,612 whole-genome triplication genes exhibiting high expression levels associated with low DNA methylation levels and high N6-methyladenosine RNA modifications. DNA methylation changes are also associated with activation of genes involved in callus formation. Conclusions Our gapless lettuce genome assembly, an unprecedented achievement in the Asteraceae family, establishes a solid foundation for functional genomics, epigenomics, and crop breeding and sheds new light on understanding the complexity of gene regulation associated with the dynamics of DNA and RNA epigenetics in genome evolution.

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Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

Cao,

Sawettalake,

Shen

2024

GigaScience

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The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood

Peng,

Hong,

Kan

et al. 2024

GigaScience

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Background Sandalwood, a prized hemiparasitic plant, is highly sought in the commercial market because of its aromatic core materia. The structure and stability of the genome are instrumental in the rapid adaptation of parasitic plants to their surroundings. However, there is a conspicuous lack of research on the genomic-level adaptive evolution of sandalwood. Results In this study, we assembled a gap-free telomere-to-telomere (T2T) reference genome for Santalum album using PacBio HiFi, Hi-C, and ultra-long ONT data. The T2T reference genome (Sal_t2t) encompassed annotations of 24,171 genes and 25.34% repetitive sequences, in addition to all 10 centromeres and 20 telomeres across the 10 chromosomes. The results revealed that the 3 distinct parasitic species of Santalales had diverse centromeric compositions. The Copia-type long terminal repeat transposon emerged as the most significant in the S. album genome, constituting the primary sequence of the centromere and influencing gene expression. Third, in sandalwood, the presence of Copia affected the size of the centromeres and, consequently, the genome size. Identification of the sandalwood T2T genome in this study also enabled the identification of more precise organelle transfer fragments. Conclusions Our research provides a sandalwood T2T genome, laying the groundwork for future investigations on the evolution of energy organs in parasitic plants. Moreover, it offers novel insights into the function and evolution of centromeres, as well as the mechanisms of adaptation and parasitism.

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Green Elegance T2T: An upgraded telomere-to-telomere genome assembly and annotation of looseleaf lettuce (Lactuca sativavar.crispa)

Zhang,

Liu,

Ding

et al. 2024

Preprint

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Lettuce (Lactuca sativa L.), a globally important vegetable crop, is cultivated in various horticultural varieties. Looseleaf lettuce is one of the main varieties that are consumed. Here, we report a telomere-to-telomere (T2T) genome assembly of looseleaf lettuce (L. sativa var. crispa cv. Green Elegance). By combining the sequencing data of previously reported Green Elegance v1.2, the 42.20 Gb clean ultra-long reads produced by Oxford Nanopore Technology were used to close the gaps and upgrade the genome assembly. After filling 11 gaps in Green Elegance v1.2, the final gapless telomere-to-telomere genome assembly is 2.58 Gb in length with a contig N50 of 282.47 Mb, containing nine centromeres and 18 telomeres. The genome contained 41,375 protein-coding genes, of which 99.10% were functionally annotated. This T2T genome of looseleaf lettuce will be valuable for the identification of genetic variation and the advancement of lettuce breeding.

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Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

Cited by 4 publications

References 98 publications

Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood

Green Elegance T2T: An upgraded telomere-to-telomere genome assembly and annotation of looseleaf lettuce (Lactuca sativavar.crispa)

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