Comparative analysis of complete chloroplast genome sequences of four major Amorphophallus species

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.

Complete plastome assemblies from a panel of 13 diverse potato taxa

“…Out of 746 overall SNP sites, only 57 SNPs are located in IR regions indicating that IR regions are more conserved than the LSC region with 519 SNPs and the SSC region with 170 SNPs. These results are in agreement with other studies [5,8]. Overall, 57 genes in total have SNPs, and a few genes have more SNPs than others.…”

“…Also, the ycf1 and the matK genes have 12 and nine InDels, respectively (S2 Fig). High divergence of the ycf1 gene has been observed in the plastomes of many plant species and this has led to it being used as a DNA barcode in land plants [5,32].…”

“…Despite the degree of plastome conservation in most land plants, many structural and single nucleotide variations have been observed. These variations include interspecies deletions [3], insertions and deletions (InDels), single nucleotide polymorphisms (SNPs), genome expansions, and polymorphic single sequence repeats (SSRs) [4,5].…”

The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): genomic features and comparative analysis with other legume genomes

“…In recent years, there has been a significant increase in the number of chloroplast genomes (cp genomes) studies due to the emergence of next-generation DNA sequencing (NGS) technologies and the advances of bioinformatics tools (Mardis 2008;Metzker 2010;Khan et al 2019;Liu et al 2019). The cp genome has maternal inheritance and generally consists of circular double-stranded DNA molecules with a size between 120 and 160 kb.…”

The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae)

“…Illumina-based NGS technology has been widely used recently, and the molecular structures of many plant cp genomes have been discovered in detail within a short period [22]. Chloroplast genomic information has been widely used for molecular marker development in different evolutionary studies [17,23]. Polymorphic simple sequence repeats (SSR) identified in the cp genomes were previously used for species identification, population genetics, and phylogenetic studies [24,25].…”