Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha

Abstract

Actinidia eriantha is a characteristic fruit tree featuring with great potential for its abundant vitamin C and strong disease resistance. It has been used in a wide range of breeding programs and functional genomics studies. Previously published genome assemblies of A. eriantha are quite fragmented and not highly contiguous. Using multiple sequencing strategies, we get the haplotype-resolved and gap-free genomes of an elite breeding line “Midao 31” (MD), termed MDHAPA and MDHAPB. The new assemblies anchored to 29 pseudochromosome pairs with a length of 619.3 Mb and 611.7 Mb, as well as resolved 27 and 28 gap-close chromosomes in a telomere-to-telomere (T2T) manner. Based on the haplotype-resolved genome, we found that most alleles experienced purifying selection and coordinately expressed. Owing to the high continuity of assemblies, we defined the centromeric regions of A. eriantha, and identified the major repeating monomer, which is designated as Ae-CEN153. This resource lays a solid foundation for further functional genomics study and horticultural traits improvement in kiwifruit. Graphical Abstract

Telomere Length in Plants Estimated with Long Read Sequencing

“…(Mca) (Fu et al ., 2023), Actinidia chinensis HY4P and HY4A (Yue et al ., 2023), Zea mays Mo17 (Chen et al ., 2023), Dianthus caryophyllus (Lan et al, 2024), Ficus hispida (Liao et al, 2024), Vaccinium duclouxii (Zeng et al, 2023), Vitis vinifera Thompson Seedless (X. Wang et al ., 2024) , Cucumis melo L. var. Inodorus (Wei et al ., 2023) ), Mangifera indica ‘Irwin’ (Henry et al preprint), Musa acuminata Wild type (Liu et al ., 2023) and Cavendish (Huang et al ., 2023), Oryza sativa ZS97RS3 and MH63RS3 (Song et al ., 2021), Mycrica rubra (Zhang et al ., 2024) (Supplemental Table S1).…”

“…Inodorus (Wei et al ., 2023) ), Mangifera indica ‘Irwin’ (Henry et al preprint), Musa acuminata Wild type (Liu et al ., 2023) and Cavendish (Huang et al ., 2023), Oryza sativa ZS97RS3 and MH63RS3 (Song et al ., 2021), Mycrica rubra (Zhang et al ., 2024) (Supplemental Table S1). However, assembled telomere sequence is often used as a means to an end in confirming a complete assembly; their details are often relegated to supplemental materials or in many cases not clearly reported at all (Belser et al ., 2021; Bao et al ., 2023; He et al ., 2023; Sato et al ., 2023; Sun et al ., 2023; Wang et al ., 2023; Bi et al ., 2024; Z. Wang et al ., 2024).…”

The high‐quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae

“…For SMRT long‐read sequencing, approximately 30‐kb DNA insert libraries were constructed using a SMART SMRTbell Template Prep Kit (PacBio, CA, USA) and sequenced on PacBio Sequel II platform. For Illumina sequencing, Nextera DNA Flex Library Prep Kit (Illumina, CA, USA) Sequencing libraries were constructed using a library construction kit (Illumina, CA, USA) and sequenced on Illumina HiSeq 2000 platform (Wang et al., 2023).…”

“…Using coding sequence (CDS) and annotation gff3 files as input data, the syntenic blocks for each pair species were identified using ‘jcvi.compara.catalog ortholog’, then the syntenic blocks were filtered using ‘jcvi.compara.synteny screen’ with default parameters. All the synonymous substitution rates ( K S ) distributions were constructed using the PAML package's yn00 program (Wang et al., 2023).…”

DcGST1, encoding a glutathione S‐transferase activated by DcMYB7, is the main contributor to anthocyanin pigmentation in purple carrot

“…It is believed that non‐purple carrots are mutated into purple carrots (Iorizzo et al., 2020; Simon, 2000). Carrots are an excellent model system for studying color variation because of their rich and colorful germplasm resources, relatively compact genome (~430 Mb) (Wang, Liu, et al., 2023), and ease of transformation (Xu, Feng, et al., 2019).…”