Products

Main analyses include:

1) T2T Genome Assembly

● T2T genome refers to a genome with “0 gaps” in which at least one chromosome is completely assembled from telomere to telomere.

● Using high-accuracy CCS reads and ONT ultra-long reads:

    * Generate contig v1 genome via hybrid assembly using hifiasm (v0.25.0).

    * Remove plastid and contaminated sequences by BLAST against the NT database.

    * Scaffold contigs into chromosome-scale assembly using Hi-C data with 3D-DNA.

    * Fill missing telomeres through local assembly with ONT reads to obtain the final T2T genome.

2) Assembly Evaluation

● BUSCO Evaluation

BUSCO v5.2.1 (Benchmarking Universal Single-Copy Orthologs) constructs single-copy gene sets for major evolutionary lineages based on the OrthoDB 10 database. The assembled genome is evaluated by alignment against this gene set, based on the matching ratio and integrity.

A higher proportion of “Complete BUSCOs” indicates higher genome assembly completeness.

● Reads Mapping

Align short reads from next-generation sequencing (e.g., Illumina) to the assembled genome using bwa. Align third-generation long reads to the assembled genome using Minimap2.

The completeness of the assembled genome and uniformity of sequencing coverage are evaluated based on mapping rate, genome coverage ratio, and depth distribution.

● Genome QC Evaluation

Evaluate the assembly using Merqury by comparing high-accuracy sequencing reads k‑mers with the genome assembly to obtain consensus quality (QV).

Higher quality values indicate higher accuracy of the assembled genome.

● Genome LAI Evaluation

LAI (LTR Assembly Index) assesses genome assembly integrity as the ratio of intact LTR retrotransposon sequences to total LTR sequences. Candidate LTR-RT sequences are identified using LTR_FINDER (v1.0.7) and LTRharvest (v1.5.9), then filtered and integrated using LTR_retriever (v2.8) to obtain high-confidence LTR retrotransposons and calculate LAI.

According to the LAI developer’s publication, LAI values are classified into three levels:

   Draft (0 ≤ LAI < 10), Reference (10 ≤ LAI < 20), and Gold (LAI ≥ 20).

● Identification of Telomeres and Centromeres

Identify potential telomere repeat units in the genome using TIDK. Detect telomere sequences and obtain positional information using FindTelomeres based on repeat motifs.

Identify potential centromeric repeats using Centromics with third‑generation long reads, then remap to the genome to obtain centromere positions and sequences.

1) Genome Chromosome Map

2) Telomere Positions in the Genome

Note:

Chr: Chromosome ID

Chr_Length (bp): Chromosome length

Upstream_Start (bp): Start position of the upstream telomere on the chromosome

Upstream_End (bp): End position of the upstream telomere on the chromosome

Upstream_Length (bp): Length of the upstream telomere on the chromosome

Downstream_Start (bp): Start position of the downstream telomere on the chromosome

Downstream_End (bp): End position of the downstream telomere on the chromosome

Downstream_Length (bp): Length of the downstream telomere on the chromosome

3) Centromere Positions in the Genome

Note:

Chr: Chromosome ID

Chr_Length (bp): Chromosome length

Centromere_Start (bp): Start position of the centromere on the chromosome

Centromere_End (bp): End position of the centromere on the chromosome

4) Gap Statistics of Assembly Results

Note:

Group: Chromosome ID  

Gap_Number: Number of gaps on the chromosome  

Len (bp): Chromosome length

5) Genome LAI Evaluation

Note: According to the publication by the LAI developers, LAI values are classified into three categories: Draft (0 ≤ LAI < 10), Reference (10 ≤ LAI < 20), and Gold (LAI ≥ 20).

Chr Length (bp): Chromosome length

Intact: Proportion of intact LTR-RTs in the genome

Total: Proportion of total LTRs in the genome

raw_LAI = Intact / Total × 100

LAI: Corrected LAI value

Explore the advancements facilitated by BMKGene’s de novo genome assembly services through a curated collection of publications:

T2T Genome

Liu, Shoucheng et al. “A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat.” Nature genetics vol. 57,4 (2025): 1008-1020. doi:10.1038/s41588-025-02137-x

Yao, Xue-Feng et al. “Complete genome assembly of japonica rice variety Zhonghua 11.” Plant communications vol. 6,10 (2025): 101463. doi:10.1016/j.xplc.2025.101463

Lv, Zhiyuan et al. “Near telomere-to-telomere genome assembly of Camellia pitardii.” Scientific data vol. 12,1 1422. 14 Aug. 2025, doi:10.1038/s41597-025-05764-5

Du, Haiyuan et al. “A near-complete genome assembly of Fragaria iinumae.” BMC genomics vol. 26,1 253. 14 Mar. 2025, doi:10.1186/s12864-025-11440-0

Chen, Weikai et al. “The complete genome assembly of Nicotiana benthamiana reveals the genetic and epigenetic landscape of centromeres.” Nature plants vol. 10,12 (2024): 1928-1943. doi:10.1038/s41477-024-01849-y

Haplotype-resolved T2T Genome

Khan, Falak Sher et al. “Haplotype-resolved T2T gap-free genomes of the winegrape cultivar Cabernet Sauvignon.” Scientific data, 10.1038/s41597-026-06910-3. 26 Feb. 2026, doi:10.1038/s41597-026-06910-3

T2T Genome + Comparative Genome

Hong, Lin et al. “Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis).” GigaScience vol. 13 (2024): giae084. doi:10.1093/gigascience/giae084

Li, Xiao-Jie et al. “Analysis of telomere-to-telomere genome of red carrot TXH4 elucidates the role of DcLCYE and DcLCYB1 in lycopene accumulation in carrot.” Horticulture research vol. 12,11 uhaf192. 29 Jul. 2025, doi:10.1093/hr/uhaf192

T2T Genome + Pangenome

Wang, Xiaojing et al. “T2T genome, pan-genome analysis, and heat stress response genes in Rhododendron species.” iMeta vol. 4,2 e70010. 5 Mar. 2025, doi:10.1002/imt2.70010