Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

Abstract

Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas XerophytaJuss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.

Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus

“…We found that the GC content in the cp genome of Pooideae species was unevenly distributed, with the IR regions having a higher GC content than the two single copy regions. This may be attributed to the fact that four rRNA genes with high GC content were located in the IR regions, which supported the speculation of previous studies ( Mardanov et al, 2008 ; Gao et al, 2009 ; Wanga et al, 2021 ). The accD gene has been lost within the cp genomes of Pooideae species, while ycf1 , ycf2 , ycf15 , and ycf68 were pseudogenes, which is a relatively common phenomenon in Poaceae ( Huang et al, 2017 ).…”

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

“…These similarities in codon choice also reveal the related relationship in the four species. The observed codon pattern is consistent with the CP genomes of Amomum [68], Panax [69], Dipterygium and Cleome [70], and various other species [71][72][73].…”

The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships

“…Codon is the connection between the nucleic acids and proteins, and codon usage reflects the preference for selective use of codons encoding specific amino acids with genetic information ( Wanga et al, 2021 ). The codon usage frequency of 79 protein-coding genes for 8 Fagopyrum species were calculated, and 64 codons were involved in encoding proteins containing three termination codons, such as UAA, UAG, and UGA ( Table 3 ).…”