Sequencing and Assembly of Polyploid Genomes

Wang, Yibin; Yu, Jiaxin; Jiang, Mengwei; Lei, Wen‐Long; Zhang, Xingtan; Tang, Haibao

doi:10.1007/978-1-0716-2561-3_23

Cited by 13 publications

(7 citation statements)

References 113 publications

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“…2C; Table S4). This is mainly due to integrated use of powerful HiFi long reads and effective Hi-C sequencing data, a strategy that has been found efficient for developing highly contiguous polyploid genome assemblies ( 44 ). Owing to the large genome size of hexaploid wheat and prohibitive sequencing costs, we did not use Nanopore sequencing technology in this work, thus missing the opportunity to obtain a telomere-to-telomere genome assembly at present.…”

Section: Discussionmentioning

confidence: 99%

A highly contiguous hexaploid wheat genome assembly facilitates analysis of 1RS translocation and mining of a new adult plant resistance locus to yellow rust disease

Li,

Ren,

Yang

et al. 2023

Preprint

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High-quality genome information is essential for efficiently deciphering and improving crop traits. Here we report a highly contiguous hexaploid genome assembly for the key wheat breeding parent Zhou8425B, an elite 1BL/1RS translocation line with durable adult plant resistance (APR) against rust diseases. By using HiFi and Hi-C sequencing reads, a 14.75 Gb genome assembly, with contig N50 and scaffold N50 values reaching 70.94 and 735.11 Mb, respectively, was developed. Comparison with 16 previously sequenced common wheat cultivars revealed unique chromosomal structural features in Zhou8425B. Notably, the 1RS translocation in Zhou8425B was apparently longer and carried more genes encoding AP2/ERF-ERF and B3 transcription factors relative to its counterpart in several genome sequenced 1BL/1RS varieties and rye lines. Aided by Zhou8425B genome assembly, a new APR locus (i.e., YrZH3B) against yellow rust (YR) disease was finely mapped to a 1 - 2 Mb interval on chromosome 3BS. Analysis with 212 Zhou8425B derivative varieties showed that pyramiding of YrZH3B with two other APR loci (YrZH22 and YrZH84) significantly decreased YR severity and enhanced grain yield, with triple combination (YrZH3B/YrZH22/YrZH84) having the highest effects. Our data demonstrate the high value of Zhou8425B assembly in studying wheat genome and agronomically important genes.

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Section: Discussionmentioning

confidence: 99%

A highly contiguous hexaploid wheat genome assembly facilitates analysis of 1RS translocation and mining of a new adult plant resistance locus to yellow rust disease

Li,

Ren,

Yang

et al. 2023

Preprint

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“…'Camarosa' was developed in 2019 (Edger et al, 2019). Before the release of the first octoploid strawberry genome, there were few genome assemblies available for polyploid species, as the homoeologous nature of the subgenomes made assembly of sequences difficult (Wang et al, 2023b). As such, molecular genetic analysis of Fragaria ×ananassa prior to 2019 relied on early genome assemblies of Fragaria vesca, the first of which was published in 2011 (Shulaev et al, 2011).…”

Section: Advanced Genomic Resources In Strawberrymentioning

confidence: 99%

“…As such, molecular genetic analysis of Fragaria ×ananassa prior to 2019 relied on early genome assemblies of Fragaria vesca, the first of which was published in 2011 (Shulaev et al, 2011). Recent rapid advancements in genome sequencing technology have resulted in the release of additional annotated octoploid genome sequences of increasing quality (Table 1) (Wang et al, 2023b). Advancements in genome sequencing in strawberry have not been limited only to the octoploid, as new high-quality genomes have also recently been released for the diploid model species, Fragaria vesca (Alger et al, 2021;Joldersma et al, 2022).…”

Section: Advanced Genomic Resources In Strawberrymentioning

confidence: 99%

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

Vondracek,

Altpeter,

Liu

et al. 2024

Front. Genet.

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The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

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“…The large and complex nature of plant genomes, coupled with varying degrees of ploidy, has long posed challenges for genome assembly in plants. Fortunately, advancements in sequencing technologies, such as third-generation long-read sequencing, particularly High Fidelity (HiFi) reads sequencing, along with new assembly algorithms serve as the foundation for the rapid advancements in plant genome sequencing (Wang et al 2023). HiFi sequencing allows for the generation of long-read, high-quality data that can be used to accurately assemble and annotate complex genomes.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale Genome Assembly of the Alloenneaploid Arundo donax

Ren,

Han,

Liu

et al. 2024

Preprint

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Arundo donax L (A. donax). is a promising energy crop with high biomass and wide adaptability, while lack of reference genome limiting the genetic improvement of this crop. Here, we report the first chromosome-scale assembly of A. donax genome using Pacbio SMRT sequencing and Hi-C technology. The genome size of this assembly is 1.30 Gb with contig N50 33.15 Mb. A total of 74,403 gene models were predicted, of which over 90% of genes were functionally annotated. Karyotype analysis and synteny analysis revealed that A. donaxis an alloenneaploid (3n = 9x = 108). Comparative genome analysis indicated that A. donax has undergone strong gene family expansion and two whole-genome duplication events during evolution. Based on the genome assembly, we mined numerous salinity stress related genes using public RNA-seq data. The genome assembly we provided in this study will enhance genetic understanding and promote the genetic improvement of A. donax.

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Sequencing and Assembly of Polyploid Genomes

Cited by 13 publications

References 113 publications

A highly contiguous hexaploid wheat genome assembly facilitates analysis of 1RS translocation and mining of a new adult plant resistance locus to yellow rust disease

A highly contiguous hexaploid wheat genome assembly facilitates analysis of 1RS translocation and mining of a new adult plant resistance locus to yellow rust disease

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

Chromosome-scale Genome Assembly of the Alloenneaploid Arundo donax

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