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Comparative chloroplast genomes of Sophora species: identification of variable DNA markers and phylogenetic relationships within the genus
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Comparative chloroplast genomes of Sophora species: identification of variable DNA markers and phylogenetic relationships within the genus
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Journal Article
Comparative chloroplast genomes of Sophora species: identification of variable DNA markers and phylogenetic relationships within the genus
2025
Overview
Backgroud
Sophora
L. is a medicinally significant genus within Papilionoideae (Fabaceae), renowned for its medicinal, ecological, and economic importance. However, taxonomic and phylogenetic uncertainties persist within this genus, especially in China, due to limited genetic data and the lack of effective molecular markers. This study aimed to address these limitations by sequencing and analyzing chloroplast (cp.) genomes from six
Sophora
species endemic to China, thereby enriching genetic resources for future research.
Result
Here, we reported and characterized six chloroplast (cp.) genomes of
Sophora
species (
Sophora xanthantha
,
Sophora davidii
,
Sophora moocroftiana
,
Sophora tonkinensis
,
Sophora velutina
, and
Sophora velutina
var.
cavaleriei
) from China, sequenced using the Illumina HiSeq platform. Comparative analyses of these newly generated cp. genomes, alongside previously published
Sophora
cp. genomes, revealed that the
Sophora
cp. genomes exhibited a size range of 151,270 − 154,378 bp (excluding
S. japonica
and
S. xanthantha
). We observed expansions of the inverted repeat (IR) regions in
Sophora
, leading to the translocation of
rpl
2 into the large single-copy (LSC) region, pseudogenization of
ycf
1, and absence of
trn
H in some species. Comparative genome analysis revealed a ~ 24-kb inversion between
trn
C-GCA and
trn
F-GAA within the genus, a phenomenon first observed to involve at least three rearrangements. Furthermore, we identified three valuable molecular markers (
trn
T
-
UGU
- trn
L
-
UAA,
psb
E
- pet
L, and
rps
11
- rpl
36) that are suitable for phylogenetic inference within
Sophora
.
Conclusions
Phylogenetic analyses based on the chloroplast genomes robustly supported the monophyly of sect.
Pseudosophora
. Importantly, our phylogenetic results suggested that
S. japonica
and
S. xanthantha
should not be classified within the genus
Sophora
. These findings contribute significantly to the chloroplast genomic data of
Sophora
and provide valuable genetic resources and molecular markers for resolving taxonomic ambiguities and advancing future phylogenetic, evolutionary, and taxonomic investigations of
Sophora
.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
