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Characterization of the complete chloroplast genome of an aquatic plant, Sparganium stoloniferum subsp. choui (Typhaceae).

ABSTRACT: Sparganium stoloniferum subsp. choui is an aquatic perennial herb distributed in Northeast China. It was published as a new species in 1992 and recognized as a subspecies of S. stoloniferum in Flora of China in 2010. The complete chloroplast genome of S. stoloniferum subsp. choui was sequenced and assembled. The genome size was 161,865 bp in length with 36.8% GC content. Its quadripartite structure consisted of the large single copy (LSC, 88,953 bp) and small single copy (SSC, 19,098 bp) regions, separated by a pair of inverted repeats (IRs) of 26,907 bp. The genome contained 114 distinct genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis including four Sparganium species showed that two subspecies of S. stoloniferum were not monophyletic, supporting the resurrection of S. choui as a species.

SUBMITTER: Huang L

PROVIDER: S-EPMC8477951 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSparganium (Typhaceae) is a widespread temperate genus of ecologically important aquatic plants. Previous reconstructions of the phylogenetic relationships among Sparganium species are incompletely resolved partly because they were based on molecular markers comprising < 7,000 bp. Here, we sequenced and assembled the complete chloroplast genomes from 19 Sparganium samples representing 15 putative species and three putative subspecies in order to explore chloroplast genome evolution in this genus, clarify taxonomic lineages, estimate the divergence times of Sparganium species, and reconstruct aspects of the biogeographic history of the genus.ResultsThe 19 chloroplast genomes shared a conserved genome structure, gene content, and gene order. Our phylogenomic analysis presented a well-resolved phylogeny with robust support for most clades. Non-monophyly was revealed in three species: S. erectum, S. eurycarpum, and S. stoloniferum. Divergence time estimates suggest that the two subgenera of Sparganium split from each other ca. 30.67 Ma in the middle Oligocene. The subgenus Xanthosparganium diversified in the late Oligocene and Miocene, while the subgenus Sparganium diversified in the late Pliocene and Pleistocene. Ancestral area reconstruction suggested that the two subgenera may have originated in East Eurasia and North America.ConclusionThe non-monophyletic nature of three putative species underscores the necessity of taxonomic revision for Sparganium: S. stoloniferum subsp. choui may be more appropriately identified as S. choui, and subspecies of S. erectum may be in fact distinct species. The estimated diversification times of the two subgenera correspond to their species and nucleotide diversities. The likely ancestral area for most of subgenus Xanthosparganium was East Eurasia and North America from where it dispersed into West Eurasia and Australia. Most of subgenus Sparganium likely originated in North America and then dispersed into Eurasia. Our study demonstrates some of the ways in which complete chloroplast genome sequences can provide new insights into the evolution, phylogeny, and biogeography of the genus Sparganium.

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Characterization of the complete chloroplast genome of an aquatic plant, Sparganium stoloniferum subsp. choui (Typhaceae).

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