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Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops.
BMC Genomics. 2020 Mar 20; 21(1):246.BG

Abstract

BACKGROUND

Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops.

RESULTS

Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and Am-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.

CONCLUSIONS

RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

Authors+Show Affiliations

Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan. kentaro.yoshida@port.kobe-u.ac.jp.Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan.Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32192452

Citation

Tanaka, Sayaka, et al. "Diploid Genome Differentiation Conferred By RNA Sequencing-based Survey of Genome-wide Polymorphisms Throughout Homoeologous Loci in Triticum and Aegilops." BMC Genomics, vol. 21, no. 1, 2020, p. 246.
Tanaka S, Yoshida K, Sato K, et al. Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops. BMC Genomics. 2020;21(1):246.
Tanaka, S., Yoshida, K., Sato, K., & Takumi, S. (2020). Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops. BMC Genomics, 21(1), 246. https://doi.org/10.1186/s12864-020-6664-3
Tanaka S, et al. Diploid Genome Differentiation Conferred By RNA Sequencing-based Survey of Genome-wide Polymorphisms Throughout Homoeologous Loci in Triticum and Aegilops. BMC Genomics. 2020 Mar 20;21(1):246. PubMed PMID: 32192452.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops. AU - Tanaka,Sayaka, AU - Yoshida,Kentaro, AU - Sato,Kazuhiro, AU - Takumi,Shigeo, Y1 - 2020/03/20/ PY - 2019/12/27/received PY - 2020/03/10/accepted PY - 2020/3/21/entrez PY - 2020/3/21/pubmed PY - 2020/12/22/medline KW - Genome differentiation KW - Genome-wide polymorphisms KW - RNA sequencing KW - Wheat SP - 246 EP - 246 JF - BMC genomics JO - BMC Genomics VL - 21 IS - 1 N2 - BACKGROUND: Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops. RESULTS: Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and Am-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species. CONCLUSIONS: RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/32192452/Diploid_genome_differentiation_conferred_by_RNA_sequencing_based_survey_of_genome_wide_polymorphisms_throughout_homoeologous_loci_in_Triticum_and_Aegilops_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6664-3 DB - PRIME DP - Unbound Medicine ER -