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

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 1, 2024

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

Язык: Английский

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

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 1, 2024

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

Язык: Английский

ND-FISH with New Oligo Probes for Chromosome Identification of Cichorium intybus Revealing Karyotypic Variation and Divergence of Asteraceae Species

Plants, Год журнала: 2024, Номер 13(22), С. 3135 - 3135

Опубликована: Ноя. 7, 2024

Chicory (

Язык: Английский