AUTHOR=Ren Weichao , Jiang Zhehui , Zhang Meiqi , Kong Lingyang , Zhang Houliang , Liu Yunwei , Fu Qifeng , Ma Wei 

TITLE=The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.987443

DOI=10.3389/fpls.2022.987443

ISSN=1664-462X

ABSTRACT=<p><italic>Salix floderusii</italic> is a rare alpine tree species in the <italic>Salix</italic> genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of <italic>S. floderusii</italic> for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The <italic>S. floderusii</italic> cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of <italic>S. floderusii</italic> and <italic>Salix caprea</italic> were shorter than those of <italic>Salix cinerea</italic>, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the <italic>rpl22</italic> coding region, <italic>psbM/trnD-GUC</italic> non-coding region, <italic>petA/psbJ</italic> non-coding region, and <italic>ycf1</italic> coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future <italic>Salix</italic> species. In addition, phylogenetic analysis indicated that the cp genome of <italic>S. floderusii</italic> is sister to <italic>Salix cupularis</italic> and belongs to the Subgenus <italic>Vetrix</italic>. Genes (Sf-<italic>trnI</italic>, Sf-<italic>PpsbA</italic>, <italic>aadA</italic>, Sf-<italic>TpsbA</italic>, Sf-<italic>trnA</italic>) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene <italic>aadA</italic>. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the <italic>aadA</italic> gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent <italic>S. floderusii</italic> cp transformation systems and developing strategies for the genetic improvement of <italic>S. floderusii.</italic></p>