Background
The genus
Amorphophallus
(Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of
Amorphophallus
is limited. In this study, four chloroplast genomes of
Amorphophallus
were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13
Amorphophallus
species in conjunction with nine published sequences.
Results
The
Amorphophallus
chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 − 98,561 bp), a small single copy (SSC, 14,172 − 21,575 bp), and a pair of inverted repeats (IRs, 26,225 − 35,204 bp). The genomes contain 108 − 113 unique genes, including 76 − 79 protein-coding genes, 28 − 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within
Amorphophallus
were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including
trnM-atpE, atpB
,
atpB-rbcL
and
ycf1
were identified. They could identify and phylogeny future species in the genus
Amorphophallus
. Positive selection was found for
rpl36
,
ccsA
,
rpl16
,
rps4
,
rps8
,
rps11
,
rps12
,
rps14
,
clpP
,
rps3
,
ycf1
,
rpl20
,
rps2
,
rps18
,
rps19, atpA
,
atpF
,
rpl14
,
rpoA
,
rpoC1
,
rpoC2
and
rps15
based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between
Amorphophallus
and
Caladieae
. All
Amorphophallus
species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I.
Amorphophallus albus
,
A. krausei
,
A. kachinensis
and
A. konjac
...