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The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads.
BMC Plant Biol 2019; 19(1):226BP

Abstract

BACKGROUND

Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives.

RESULTS

Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes.

CONCLUSIONS

The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.

Authors+Show Affiliations

Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. liuqing@scib.ac.cn.Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. University of Chinese Academy of Sciences, Beijing, China.Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. University of Chinese Academy of Sciences, Beijing, China.Genepioneer Biotechnologies Co. Ltd., Nanjing, China.Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. phh4@le.ac.uk. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK. phh4@le.ac.uk.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31146681

Citation

Liu, Qing, et al. "The Repetitive DNA Landscape in Avena (Poaceae): Chromosome and Genome Evolution Defined By Major Repeat Classes in Whole-genome Sequence Reads." BMC Plant Biology, vol. 19, no. 1, 2019, p. 226.
Liu Q, Li X, Zhou X, et al. The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC Plant Biol. 2019;19(1):226.
Liu, Q., Li, X., Zhou, X., Li, M., Zhang, F., Schwarzacher, T., & Heslop-Harrison, J. S. (2019). The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC Plant Biology, 19(1), p. 226. doi:10.1186/s12870-019-1769-z.
Liu Q, et al. The Repetitive DNA Landscape in Avena (Poaceae): Chromosome and Genome Evolution Defined By Major Repeat Classes in Whole-genome Sequence Reads. BMC Plant Biol. 2019 May 30;19(1):226. PubMed PMID: 31146681.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. AU - Liu,Qing, AU - Li,Xiaoyu, AU - Zhou,Xiangying, AU - Li,Mingzhi, AU - Zhang,Fengjiao, AU - Schwarzacher,Trude, AU - Heslop-Harrison,John Seymour, Y1 - 2019/05/30/ PY - 2018/12/26/received PY - 2019/04/09/accepted PY - 2019/6/1/entrez PY - 2019/5/31/pubmed PY - 2019/7/13/medline KW - Chromosome evolution KW - Common oat (Avena sativa) KW - Fluorescence in situ hybridization (FISH)-based karyotypes KW - Genome-specific markers KW - Intergenomic translocations KW - Repetitive DNAs SP - 226 EP - 226 JF - BMC plant biology JO - BMC Plant Biol. VL - 19 IS - 1 N2 - BACKGROUND: Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS: Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS: The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/31146681/The_repetitive_DNA_landscape_in_Avena__Poaceae_:_chromosome_and_genome_evolution_defined_by_major_repeat_classes_in_whole_genome_sequence_reads_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-1769-z DB - PRIME DP - Unbound Medicine ER -