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Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny
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Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny
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Journal Article
Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny
2024
Overview
The chloroplast (cp.) genome, also known as plastome, plays crucial roles in plant survival, adaptation, and evolution. The stable genetic structure of cp. genomes provides an ideal system for investigating species evolution. We sequenced three complete cp. genome sequences of Capsicum species and analyzed them using sequences of various Capsicum species retrieved from the NCBI database. The cp. genome of
Capsicum
species maintains a well-preserved quadripartite structure consisting of two inverted repeats (IRs) flanked by a large single copy (LSC) region and a small single copy (SSC) region. The sizes of cp. genome sequences ranged from 156,583 bp (
C. lycianthoides
) to 157,390 bp (
C.pubescens
). A total of 127–132 unique genes, including 83–87 protein-coding, 36–37 tRNA, and eight rRNA genes, were predicted. Comparison of cp. genomes of 10
Capsicum
species revealed high sequence similarity in genome-wide organization and gene arrangements. Fragments of
trnT
-
UGU
/
trnL
-
UAA
,
ccsA
,
ndhD
,
rps12
, and
ycf1
were identified as variable regions, and nucleotide variability of LSC and SSC was higher than that of IR. Phylogenetic speciation analysis showed that the major domesticated
C. annuum
species were the most extensively divergent species and closely related to
C. tovarii
and
C. frutescens
. Analysis of divergent times suggested that a substantial range of speciation events started occurring ~ 25.79 million years ago (Mya). Overall, comparative analysis of cp. genomes of
Capsicum
species not only offers new insights into their genetic variation and phylogenetic relationships, but also lays a foundation for evolutionary history, genetic diversity, conservation, and biological breeding of
Capsicum
species.
