Chromosome-scale genome sequence assemblies of the 'Autumn Bliss' and 'Malling Jewel' cultivars of the highly heterozygous red raspberry (Rubus idaeus L.) derived from long-read Oxford Nanopore sequence data

被引：6

作者：

Price, R. Jordan ^{[1
]}

Davik, Jahn ^{[2
]}

Fernandez, Felicidad Fernandez ^{[3
]}

Bates, Helen J. ^{[1
]}

Lynn, Samantha ^{[3
]}

Nellist, Charlotte F. ^{[1
]}

Buti, Matteo ^{[4
]}

Roen, Dag ^{[5
]}

Surbanovski, Nada ^{[3
]}

Alsheikh, Muath ^{[5
]}

Harrison, Richard J. ^{[1
]}

Sargent, Daniel James ^{[3
]}

机构：

[1] NIAB, Cambridge Crop Res, Cambridge, England

[2] Norwegian Inst Bioecon Res, Div Biotechnol & Plant Hlth, As, Norway

[3] NIAB, Dept Genet Genom & Breeding, Kent, England

[4] Univ Florence, Dept Agr Food Environm & Forestry DAGRI, Florence, Italy

[5] Graminor Breeding Ltd, Ridabu, Norway

来源：

PLOS ONE | 2023年 / 18卷 / 05期

关键词：

ANNOTATION; CYTOSCAPE; ALIGNMENT;

D O I：

10.1371/journal.pone.0285756

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Red raspberry (Rubus idaeus L.) is an economically valuable soft-fruit species with a relatively small (similar to 300 Mb) but highly heterozygous diploid (2n = 2x = 14) genome. Chromosome-scale genome sequences are a vital tool in unravelling the genetic complexity controlling traits of interest in crop plants such as red raspberry, as well as for functional genomics, evolutionary studies, and pan-genomics diversity studies. In this study, we developed genome sequences of a primocane fruiting variety ('Autumn Bliss') and a floricane variety ('Malling Jewel'). The use of long-read Oxford Nanopore Technologies sequencing data yielded long read lengths that permitted well resolved genome sequences for the two cultivars to be assembled. The de novo assemblies of 'Malling Jewel' and 'Autumn Bliss' contained 79 and 136 contigs respectively, and 263.0 Mb of the 'Autumn Bliss' and 265.5 Mb of the 'Malling Jewel' assembly could be anchored unambiguously to a previously published red raspberry genome sequence of the cultivar 'Anitra'. Single copy ortholog analysis (BUSCO) revealed high levels of completeness in both genomes sequenced, with 97.4% of sequences identified in 'Autumn Bliss' and 97.7% in 'Malling Jewel'. The density of repetitive sequence contained in the 'Autumn Bliss' and 'Malling Jewel' assemblies was significantly higher than in the previously published assembly and centromeric and telomeric regions were identified in both assemblies. A total of 42,823 protein coding regions were identified in the 'Autumn Bliss' assembly, whilst 43,027 were identified in the 'Malling Jewel' assembly. These chromosome-scale genome sequences represent an excellent genomics resource for red raspberry, particularly around the highly repetitive centromeric and telomeric regions of the genome that are less complete in the previously published 'Anitra' genome sequence.

引用

页数：17