Comparative genomics revealed new insights into the plastome evolution of Ludwigia (Onagraceae, Myrtales)

The primrose-willow (Ludwigia L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including Ludwigia adscendens, Ludwigia hyssopifolia...

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Bibliographic Details
Published in:Science progress (1916) 2024-07, Vol.107 (3), p.368504241272741
Main Authors: Nguyen, Hoang Danh, Do, Hoang Dang Khoa, Vu, Minh Thiet
Format: Article
Language:English
Subjects:
Base Composition
Chloroplasts
Conditional probability
Evolution, Molecular
Genes
Genome, Chloroplast - genetics
Genomes
Genomics
Inverted repeat
Ludwigia
Ludwigia hyssopifolia
Nucleotides
Onagraceae
Onagraceae - classification
Onagraceae - genetics
Phylogenetics
Phylogeny
Reconstruction
rRNA
Species
tRNA
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Summary:The primrose-willow (Ludwigia L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including Ludwigia adscendens, Ludwigia hyssopifolia, and Ludwigia prostrata. Three Ludwigia cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the Ludwigia cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in Oenothera, Chamaenerion, and Epilobium genera, with primitive IR structures in Ludwigia and Circeae genera. The regions clpP, ycf2, and ycf1 genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that Ludwigia (including L. adscendens, L. hyssopifolia, L. prostrata, and Ludwigia octovalvis) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three Ludwigia species, which can be used for species identification and phylogenetic reconstruction of Ludwigia and Onagraceae taxa.
ISSN:0036-8504
2047-7163
2047-7163
DOI:10.1177/00368504241272741