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Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence
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Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence
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Journal Article
Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence
2023
Overview
Background
Pueraria montana
var.
lobata
(kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships between
Pueraria montana
var.
lobata
and the other two varieties (
P. montana
var.
thomsonii
and
P. montana
var.
montana
) remain debated. Although there is increasing evidence showing that
P. montana
var.
lobata
adapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes between
P. montana
var.
lobata
and its closely related taxa.
Results
26 newly sequenced chloroplast genomes of
Pueraria
accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of
P. montana
, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of
Pueraria
and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven
P. montana
var.
lobata
, 14
P. montana
var.
thomsonii
and six
P. montana
var.
montana
. Phylogenetic analysis revealed that
P. montana
var.
lobata
and
P. montana
var.
thomsonii
formed a clade, while all sampled
P. montana
var.
montana
formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (
accD, ndhB, ndhC, rpl2, rpoC2
, and
rps2
) that account for among-site variation in selective constraint under the clade model between accessions of the
Pueraria montana
var.
lobata
clade and the
Pueraria montana
var.
montana
clade.
Conclusion
Our data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to
P. montana
var.
lobata
and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of
P. montana
come from loci that own moderate variation and underwent modest selection.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
