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Identification of genome size and heterozygosity in 510 Jujube (Ziziphus jujuba Mill.) germplasms based on deep resequencing
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DOI：10.3389/fpls.2026.1777223.png)
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Abstract
En 中文
IntroductionGenome size and heterozygosity represent the fundamental genetic attributes of a species; but their intraspecies diversity and evolution remain largely elusive.MethodsTo address this; we developed a deep-resequencing-based approach for genome estimation by optimizing resequencing depth (30×) and kmer value (21) in Chinese jujube (Ziziphus jujuba Mill.) to achieve the best balance among accuracy; stability; and cost. Using this optimized pipeline; we estimated genome size and heterozygosity across a large panel of jujube accessions.ResultsWe estimated the genome size of 296 cultivated jujube genotypes from 293 to 409 Mb (mean 347 Mb; CV 5.94%) with heterozygosity of 1.30% to 2.01% (mean 1.72%; CV 8.21%); for 214 wild jujube; genome size varies between 311 and 391 Mb (mean 339 Mb; CV 3.40%); and heterozygosity 1.22% to 2.13% (mean 1.74%; CV 6.79%). Additionally; analyzing 798 jujube accessions with resequencing data in NCBI (using k-mer 21) revealed that low sequencing depths (10∼20×) of most accessions (98.61%) results in underestimated genome sizes (4.30–309 Mb) and overestimated heterozygosity (2.17-11.8%). Shannon-Wiener Index analysis for genome heterozygosity and size in jujube indicate a medium diversity level with cultivated jujube higher that wild one. Both genome size and heterozygosity show normal distribution; and there is a significant negative correlation between them.DiscussionDuring domestication from wild to cultivated jujube; average genome size increased by 8 Mb; while heterozygosity slightly decreased. A reference standard for genome size and heterozygosity is proposed and jujube is characterized as a small genome with mediumtohigh heterozygosity. This study establishes a powerful approach for estimating genome characteristics; enriched genomic resources for jujube; and provides insights for plant intraspecific genome diversity and evolution.
Keywords:
classification
jujube
genome size
k-mer analysis
genome heterozygosity
resequencing depth
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