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Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)

Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties coll...

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Autores principales: Liu, Xiao-fei, Sun, Ying-bo, Zhu, Gen-fa, Huang, Li-li, Yu, Bo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355175/
https://www.ncbi.nlm.nih.gov/pubmed/35930553
http://dx.doi.org/10.1371/journal.pone.0271335
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author Liu, Xiao-fei
Sun, Ying-bo
Zhu, Gen-fa
Huang, Li-li
Yu, Bo
author_facet Liu, Xiao-fei
Sun, Ying-bo
Zhu, Gen-fa
Huang, Li-li
Yu, Bo
author_sort Liu, Xiao-fei
collection PubMed
description Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties collected from the market during breeding. In this study, we analyzed the chloroplast genomes of Hippeastrum ‘Milady’, H. alberti, and H. reticulatum using the Illumina NovaSeq sequencing platform and generated full-length sequences of 158,067, 158,067, and 158,522 bp, respectively. All three genomes had the typical tetrad structure. The large single copy, small single copy, and inverted repeat regions of H. reticulatum were observed to be respectively 277, 138, and 20 bp longer than the corresponding regions of H. ‘Milady’ and H. alberti. The results of comparative analysis of simple sequence repeats (SSRs), Ka/Ks ratios, codon preferences, and complete sequences of chloroplasts of these three taxa and 14 other plant species were as follows. First, the chloroplast genomes of H. ‘Milady’, H. alberti, and H. reticulatum contain 209, 209, and 211 SSR sites, respectively, most of which (123, 123, and 122, respectively) are single nucleotide repeats. Second, leucine, arginine, and serine are the most frequently used amino acids in the three chloroplast genomes. Third, H. ‘Milady’, H. alberti, and H. reticulatum are more closely related to Lycoris and Narcissus than to Allium and Agapanthus. Our results will provide information on the study of origins or relatedness of native species, and the identification of cultivars.
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spelling pubmed-93551752022-08-06 Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae) Liu, Xiao-fei Sun, Ying-bo Zhu, Gen-fa Huang, Li-li Yu, Bo PLoS One Research Article Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties collected from the market during breeding. In this study, we analyzed the chloroplast genomes of Hippeastrum ‘Milady’, H. alberti, and H. reticulatum using the Illumina NovaSeq sequencing platform and generated full-length sequences of 158,067, 158,067, and 158,522 bp, respectively. All three genomes had the typical tetrad structure. The large single copy, small single copy, and inverted repeat regions of H. reticulatum were observed to be respectively 277, 138, and 20 bp longer than the corresponding regions of H. ‘Milady’ and H. alberti. The results of comparative analysis of simple sequence repeats (SSRs), Ka/Ks ratios, codon preferences, and complete sequences of chloroplasts of these three taxa and 14 other plant species were as follows. First, the chloroplast genomes of H. ‘Milady’, H. alberti, and H. reticulatum contain 209, 209, and 211 SSR sites, respectively, most of which (123, 123, and 122, respectively) are single nucleotide repeats. Second, leucine, arginine, and serine are the most frequently used amino acids in the three chloroplast genomes. Third, H. ‘Milady’, H. alberti, and H. reticulatum are more closely related to Lycoris and Narcissus than to Allium and Agapanthus. Our results will provide information on the study of origins or relatedness of native species, and the identification of cultivars. Public Library of Science 2022-08-05 /pmc/articles/PMC9355175/ /pubmed/35930553 http://dx.doi.org/10.1371/journal.pone.0271335 Text en © 2022 Liu et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Liu, Xiao-fei
Sun, Ying-bo
Zhu, Gen-fa
Huang, Li-li
Yu, Bo
Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)
title Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)
title_full Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)
title_fullStr Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)
title_full_unstemmed Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)
title_short Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)
title_sort complete chloroplast genomes and comparative analyses of hippeastrum ‘milady’, hippeastrum albertii and hippeastrum reticulatum (amaryllidaceae)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355175/
https://www.ncbi.nlm.nih.gov/pubmed/35930553
http://dx.doi.org/10.1371/journal.pone.0271335
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