Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex

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 informati...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autor principal:	Yong-Bi Fu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8024319122e8411fa7c6aa2c3f7bbabc
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:8024319122e8411fa7c6aa2c3f7bbabc
record_format	dspace
spelling	oai:doaj.org-article:8024319122e8411fa7c6aa2c3f7bbabc2021-12-02T16:06:45ZCharacterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex10.1038/s41598-021-94649-92045-2322https://doaj.org/article/8024319122e8411fa7c6aa2c3f7bbabc2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94649-9https://doaj.org/toc/2045-2322Abstract 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.Yong-Bi FuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yong-Bi Fu Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
description	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.
format	article
author	Yong-Bi Fu
author_facet	Yong-Bi Fu
author_sort	Yong-Bi Fu
title	Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
title_short	Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
title_full	Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
title_fullStr	Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
title_full_unstemmed	Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
title_sort	characterizing chloroplast genomes and inferring maternal divergence of the triticum–aegilops complex
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8024319122e8411fa7c6aa2c3f7bbabc
work_keys_str_mv	AT yongbifu characterizingchloroplastgenomesandinferringmaternaldivergenceofthetriticumaegilopscomplex
_version_	1718384851171672064

Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex

Ejemplares similares