The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Abstract

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

“…The trnK-UUU gene has the longest intron (2524 bp) among 18 genes and contains the matK gene inside completely. This phenomenon had been reported in other plants [53,54].…”

“…Serine (6.01%), arginine (6.00%), and leucine (6.00%) are the three most abundant amino acids, whereas methionine (1.00%) and tryptophan (1.00%) are the two least abundant amino acids. As the most abundant amino acid, a preference for leucine was also observed in other reported angiosperm chloroplast genomes [54,61], which have been frequently reported in other angiosperm taxa [62,63]. Interestingly, the majority of the RSCU values with A/T-ending codons are more than one (RSCU > 1.00), while the majority of the RSCU values with C/G-ending codons were less than one (RSCU < 1.00).…”

The complete chloroplast genome of Artocarpus altilis (Moraceae) and phylogenetic relationships

“…Nine of the protein-coding genes and six tRNAs each contained one intron, while three genes each contained two introns. In general, the gene content, order, and organization of the A. altilis cp genome is highly similar to that of the closely related A. camansi (Souza et al 2020) and A. heterophyllus (Liu et al 2017), reported previously.…”

“…In general, the gene content, order, and organization of the A. altilis cp genome is highly similar to that of the closely related A. camansi (Souza et al. 2020 ) and A. heterophyllus (Liu et al. 2017 ), reported previously.…”

“…Nowadays, with the advent of next-generation sequencing technologies (NGS), the field of chloroplast (cp) genetics and genomics has expanded dramatically (Souza et al 2019;Souza et al 2020;Mehmood et al 2020). At the present time, approximately 4896 complete plant cp genomes have been deposited as RefSeq in the NCBI Organelle Genome database (December 2020), although 17 of these species belong to the Moraceae family and only two to the Artocarpus genus.…”