Abstract
Amorphophallus (Araceae) contains more than 170 species that are mainly distributed in Asia and Africa. Because the bulbs of Amorphophallus are rich in glucomannan, they have been widely used in food, medicine, the chemical industry and so on. To better understand the evolutionary relationships and mutation patterns in the chloroplast genome of Amorphophallus, the complete chloroplast genomes of four species were sequenced. The chloroplast genome sequences of A. albus, A. bulbifer, A. konjac and A. muelleri ranged from 162,853 bp to 167,424 bp. The A. albus chloroplast (cp) genome contains 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The A. bulbifer cp genome contains 111 genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A. muelleri contains 111 and 113 genes, comprising 78 and 80 protein-coding genes, respectively, 29 tRNA genes and 4 rRNA genes. The IR (inverted repeat) region/LSC (long single copy) region and IR/SSC (short single copy) region borders of the four Amorphophallus cp genomes were compared. In addition to some genes being deleted, variations in the copy numbers and intron numbers existed in some genes in the four cp genomes. One hundred thirty-four to 164 SSRs (simple sequence repeats) were detected in the four cp genomes. In addition, the highest mononucleotide SSRs were composed of A and T repeat units, and the majority of dinucleotides were composed of AT and TA. SNPs (single nucleotide polymorphisms) and indels (insertion-deletions) were calculated from coding genes and noncoding genes, respectively. These divergences comprising SSRs, SNPs and indel markers will be useful in testing the maternal inheritance of the chloroplast genome, identifying species differentiation and even in breeding programs. Furthermore, the regression of ndhK was detected from four Amorphophallus cp genomes in our study. Complete cp genome sequences of four Amorphophallus species and other plants were used to perform phylogenetic analyses. The results showed that Amorphophallus was clustered in Araceae, and Amorphophallus was divided into two clades; A. albus and A. konjac were clustered in one clade, and A. bulbifer and A. muelleri were clustered in another clade. Phylogenetic analysis among the Amorphophallus genus was conducted based on matK and rbcL. The phylogenetic trees showed that the relationships among the Amorphophallus species were consistent with their geographical locations. The complete chloroplast genome sequence information for the four Amorphophallus species will be helpful for elucidating Amorphophallus phylogenetic relationships.
Highlights
The Amorphophallus (Araceae) genus contains more than 170 species, mainly distributed throughout Asia and Africa
2G of data for each cp genome was obtained with a 300 bp read length
Gap closing was based on the sequence of the complete cp genome from Colocasia esculenta (NC_016753)[19]
Summary
The Amorphophallus (Araceae) genus contains more than 170 species, mainly distributed throughout Asia and Africa. Zhang et al reported sequences for five Epimedium species cp genomes, which provided valuable genetic information for accurately identifying species and assisted in the utilization of Epimedium plants[15] These complete cp genome sequences have been widely used in the development of molecular markers for phylogenetic research[16,17]. This study had four aims: (1) determine the size range and structure of four Amorphophallus species cp genomes; (2) compare the variations of simple sequence repeats (SSRs) among four major Amorphophallus cp genomes; (3) examine the indels and SNPs among four major Amorphophallus cp genomes; (4) confirm the phylogenetic relationship among four Amorphophallus species, as well as other species, using the complete cp genomes These results will provide valuable and basic sequence information for taxonomic study and the development of molecular markers for further species identification of Amorphophallus. Based on the differences in the gene sequences of the four cp genomes, a DNA barcode can be developed to allow for the building of an efficient platform for postgenomics species research, such as subsequent gene excavation and functional verification of DNA sequence information
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
