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Characterizing chloroplast genomes and inferring maternal divergence of the Triticum-Aegilops complex.
Sci Rep. 2021 07 28; 11(1):15363.SR

Abstract

The Triticum (wheat)-Aegilops (goatgrass) complex has been extensively studied, but the evolutionary history of polyploid wheats has not been fully elucidated. The chloroplast (cp) with maternal inheritance and homoplasy can simplify the sequence-based evolutionary inferences, but informative inferences would require a complete and accurate cp genome sequence. In this study, 16 cp genomes representing five Aegilops and 11 Triticum species and subspecies were sequenced, assembled and annotated, yielding five novel circular cp genome sequences. Analyzing the assembled cp genomes revealed no marked differences in genome structure and gene arrangement across the assayed species. A polymorphism analysis of 72 published cp genome sequences representing 10 Aegilops and 15 Triticum species and subspecies detected 1183 SNPs and 1881 SSRs. More than 80% SNPs detected resided on the downstream and upstream gene regions and only 2.78% or less SNPs were predicted to be deleterious. The largest nucleotide diversity was observed in the short single-copy genomic region. Relatively weak selection pressure on cp coding genes was detected. Different phylogenetic analyses confirmed that the maternal divergence of the Triticum-Aegilops complex had three deep lineages each representing a diploid species with nuclear A, B, or D genome. Dating the maternal divergence yielded age estimates of divergence that matched well with those reported previously. The divergence between emmer and bread wheats occurred at 8200-11,200 years ago. These findings are useful for further genomic studies, provide insight into cp genome evolvability and allow for better understanding of the maternal divergence of the Triticum-Aegilops complex.

Authors+Show Affiliations

Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. yong-bi.fu@agr.gc.ca.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34321524

Citation

Fu, Yong-Bi. "Characterizing Chloroplast Genomes and Inferring Maternal Divergence of the Triticum-Aegilops Complex." Scientific Reports, vol. 11, no. 1, 2021, p. 15363.
Fu YB. Characterizing chloroplast genomes and inferring maternal divergence of the Triticum-Aegilops complex. Sci Rep. 2021;11(1):15363.
Fu, Y. B. (2021). Characterizing chloroplast genomes and inferring maternal divergence of the Triticum-Aegilops complex. Scientific Reports, 11(1), 15363. https://doi.org/10.1038/s41598-021-94649-9
Fu YB. Characterizing Chloroplast Genomes and Inferring Maternal Divergence of the Triticum-Aegilops Complex. Sci Rep. 2021 07 28;11(1):15363. PubMed PMID: 34321524.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Characterizing chloroplast genomes and inferring maternal divergence of the Triticum-Aegilops complex. A1 - Fu,Yong-Bi, Y1 - 2021/07/28/ PY - 2021/02/12/received PY - 2021/07/13/accepted PY - 2021/7/29/entrez PY - 2021/7/30/pubmed PY - 2021/11/3/medline SP - 15363 EP - 15363 JF - Scientific reports JO - Sci Rep VL - 11 IS - 1 N2 - The Triticum (wheat)-Aegilops (goatgrass) complex has been extensively studied, but the evolutionary history of polyploid wheats has not been fully elucidated. The chloroplast (cp) with maternal inheritance and homoplasy can simplify the sequence-based evolutionary inferences, but informative inferences would require a complete and accurate cp genome sequence. In this study, 16 cp genomes representing five Aegilops and 11 Triticum species and subspecies were sequenced, assembled and annotated, yielding five novel circular cp genome sequences. Analyzing the assembled cp genomes revealed no marked differences in genome structure and gene arrangement across the assayed species. A polymorphism analysis of 72 published cp genome sequences representing 10 Aegilops and 15 Triticum species and subspecies detected 1183 SNPs and 1881 SSRs. More than 80% SNPs detected resided on the downstream and upstream gene regions and only 2.78% or less SNPs were predicted to be deleterious. The largest nucleotide diversity was observed in the short single-copy genomic region. Relatively weak selection pressure on cp coding genes was detected. Different phylogenetic analyses confirmed that the maternal divergence of the Triticum-Aegilops complex had three deep lineages each representing a diploid species with nuclear A, B, or D genome. Dating the maternal divergence yielded age estimates of divergence that matched well with those reported previously. The divergence between emmer and bread wheats occurred at 8200-11,200 years ago. These findings are useful for further genomic studies, provide insight into cp genome evolvability and allow for better understanding of the maternal divergence of the Triticum-Aegilops complex. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/34321524/Characterizing_chloroplast_genomes_and_inferring_maternal_divergence_of_the_Triticum_Aegilops_complex_ L2 - https://doi.org/10.1038/s41598-021-94649-9 DB - PRIME DP - Unbound Medicine ER -