SAMN39213513
External Id
Huazhong Agricultural University
INSDC center name
2025-04-01T00:52:19.223Z
INSDC first public
2025-04-01T00:52:19.223Z
INSDC last update
live
INSDC status
Plant
NCBI submission model
Plant.1.0
NCBI submission package
seedling
age
2022-05
collection_date
Complex repetitive sequences of plant genome are critical for driving evaluation and regulating genes expression; however, research on complex repetitive sequences is extremely dependent on the quality of genome. Here, integrating the Oxford Nanopore and PacBio technologies, we de novo assemble a complete genome of Cucurbita maxima. This results in a total of 345.20 Mb genome with a contig N50 of 16.49 Mb. Of which, eighteen of twenty chromosomes were represented by a single contig and all chromosomes reached a gap-free level. This complete genome exhibits obvious advantages in dissection of complex repetitive sequences, which enabled us to successfully localize 40 telomeres, 20 centromeres and segmental duplications (SDs). We have identified six types of centromeric monomers in centromeres based on their diverse length. Further observation of centromeres showed that the centromeres were mainly composed of these monomers and some transposon elements. Analysis on insertion time of intact LTR retrotransposons (LTR-RTs), we found that the average insertion time of intact LTR-RTs in centromeres was earlier than that in non-centromeres, which indicated rapider evolution of centromeres. In addition, we found that the genes within the SDs were enriched in pathways related to stress tolerance, while genes of other representative cucurbit crops within SDs showed no enrichment in stress-related pathway genes, suggesting that SDs contributed to the growth and stress adaption. Collectively, our finding firstly revealed the structure and function of the centromere regions and SDs in C. maxima, which providing useful insights into the complex structure and genetic breeding of C. maxima.
description
China: Wuhan
geo_loc_name
HiFi sequencing
isolate
Cucurbita maxima
http://purl.obolibrary.org/obo/NCBITaxon_3661
organism
leaf
tissue
Plant sample from Cucurbita maxima
title