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

IF 10.6 Q1 HORTICULTURE Molecular Horticulture Pub Date : 2023-02-17 DOI:10.1186/s43897-023-00052-5

Yingzhen Wang, Minhui Dong, Ying Wu, Feng Zhang, Wangmei Ren, Yunzhi Lin, Qinyao Chen, Sijia Zhang, Junyang Yue, Yongsheng Liu

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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.

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猕猴桃端粒到端粒和单倍型解析基因组。

尼日利亚猕猴桃具有丰富的维生素C和较强的抗病性，是一种极具潜力的特色果树。它已被广泛用于育种计划和功能基因组学研究。以前发表的A.eriantha基因组组装是相当零散的，并且不是高度连续的。采用多种测序策略，我们获得了一个名为MDHAPA和MDHAPB的优良育种系“米稻31”（MD）的单倍型解析和无缺口基因组。新的组装体锚定在29对长度分别为619.3Mb和611.7Mb的假染色体上，并以端粒到端粒（T2T）的方式解析了27条和28条间隙紧密的染色体。基于单倍型解析的基因组，我们发现大多数等位基因经历了纯化选择并协同表达。由于组装体的高度连续性，我们定义了A.eriantha的着丝粒区域，并鉴定了主要的重复单体，命名为Ae-CEN153。该资源为进一步开展猕猴桃功能基因组学研究和园艺性状改良奠定了坚实的基础。

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来源期刊

Molecular Horticulture horticultural research-

CiteScore

8.00

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： Aims Molecular Horticulture aims to publish research and review articles that significantly advance our knowledge in understanding how the horticultural crops or their parts operate mechanistically. Articles should have profound impacts not only in terms of high citation number or the like, but more importantly on the direction of the horticultural research field. Scope Molecular Horticulture publishes original Research Articles, Letters, and Reviews on novel discoveries on the following, but not limited to, aspects of horticultural plants (including medicinal plants): ▪ Developmental and evolutionary biology ▪ Physiology, biochemistry and cell biology ▪ Plant-microbe and plant-environment interactions ▪ Genetics and epigenetics ▪ Molecular breeding and biotechnology ▪ Secondary metabolism and synthetic biology ▪ Multi-omics dealing with data sets of genome, transcriptome, proteome, metabolome, epigenome and/or microbiome. The journal also welcomes research articles using model plants that reveal mechanisms and/or principles readily applicable to horticultural plants, translational research articles involving application of basic knowledge (including those of model plants) to the horticultural crops, novel Methods and Resources of broad interest. In addition, the journal publishes Editorial, News and View, and Commentary and Perspective on current, significant events and topics in global horticultural fields with international interests.