Salix
, an economically and ecologically multifunctional tree species widely distributed in China, encompasses five ornamental species sequenced in this study, which are highly beneficial for plant phytoremediation due to their ability to absorb heavy metals. This research utilized high-throughput sequencing to acquire chloroplast genome sequences of
Salix
, analyzing their gene composition and structural characteristics, identifying potential molecular markers, and laying a foundation for
Salix
identification and resource classification. Chloroplast DNA was extracted from the leaves of
Salix argyracea
,
Salix dasyclados
,
Salix eriocephala
,
Salix integra
‘Hakuro Nishiki’, and
Salix suchowensis
using an optimized CTAB method. Sequencing was conducted on the Illumina NovaSeq PE150 platform, and bioinformatics tools were employed to compare the structural features and variations within the chloroplast genomes of the
Salix
. Analysis revealed high similarity among the chloroplast genome sequences of the five
Salix
species, with a subsequent examination identifying 276, 269, 270, 273, and 273 SSR loci, respectively, along with unique simple repeat sequences in each variety. Comparison of chloroplast genomes across 22
Salix
highlighted variations in regions such as
matK-trnQ
,
ndhC-trnV
,
psbE-petL
,
rpl36-rps8
, and
ndhB-rps7
, which may serve as valuable molecular markers for willow resource classification studies. In this study, chloroplast genome sequencing and structural analysis of
Salix
not only enhances the genetic resources of
Salix
but also forms a critical basis for the development of molecular markers and the exploration of interspecific phylogeny in the genus.
Supplementary Information
The online version contains supplementary material available at 10.1038/s41598-024-79604-8.