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Products introduction

Haplotype-resolved genome assembly is an emerging research method for highly heterozygous diploid or polyploid species. Traditional genome assembly algorithms tend to collapse heterozygous or homologous regions when dealing with such species, resulting in chimeric genomes. However, this approach often overlooks differences between homologous chromosomes, leading to incomplete annotations and hindering downstream analysis and precision breeding.

For species such as highly heterozygous diploid and polyploid plant, developing new solutions, especialy by integrating new sequenci

ng technologies and bioinformatics algorithms, to perform haplotype-resolved genome assembly and combining the latest assembly strategies of T2T gap-free genomes to achieve haplotype-resolved T2T genome assembly, is a necessary prerequisite for downstream analysis and precision breeding of such species.


Technology roadmap


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Application direction

  • Research on hybrid vigor

  • Origin and evolution studies

  • Subgenomic differences comparison

  • Molecular breeding


Sequencing strategy:

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Benagen advantage:

  1. Independently developed Nanopore ultra-long extraction kit.

  2. Independently developed T2T genome assembly method, and obtained a patent.

  3. Proficient in sequencing around 200 species utilizing Nanopore ultra-long sequencing technology, with contributions to approximately 20 published articles.


Project Case


Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube(Horticulture Research,2024.03,IF=7.6)


Benagen is involved in the high quality haplotype-resolved T2T genome sequencing and assembly work of this project.


Materials: Jujube (JZ) and wild jujube accession (SZ)


Methods: Illumina, PacBio HiFi, ONT, Hi-C, RNA-seq, resequencing


Research Content:

(1) Based on ONTultra-long sequencing (N50>100K), HIFI, Hi-C data, the haplotype T2T-level genomes of jujube and wild jujube were constructed;

(2) The subgenomes of jujube and wild jujube were aligned and identified for structural variations against the newly published DZV2 genome. Through functional enrichment analysis, genes affected by SVs related to lipid decomposition metabolism, starch and sucrose metabolism, and other processes were revealed;

(3) Allelic genes were identified, and ASEGS genes were identified based on RNA-seq data from different maturity periods. Further findings showed differences in the biological processes where differentially expressed allelic genes are mainly concentrated in jujube and wild jujube;

(4) Population analysis was carried out on resequencing data of 672 samples to explore the population structures of jujube and wild jujube.

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Haplotype-resolved T2T genome related literature collection(Incomplete statistics)

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Reference

Li K, Chen R, Abudoukayoumu A, et al. Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube. Hortic Res. 2024.


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