The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree

Abstract

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…Of the 27,427-27,669 codons, leucine (Leu) was the most abundant amino acid, with a frequency of 10.34%-10.38%, then isoleucine (Ile) with a frequency of 8.74%-8.80%, while cysteine (Cys) was the least common one with a proportion of 1.12%-1.13% ( Figure 2 and Table S4). This phenomenon was consistent with other land plants' chloroplast genomes, such as Z. officinale [25], Ailanthus altissima [35], Lycium chinense [36], Symplocarpus renifolius [37], and Epipremnum aureum [38]. Due to the value of relative synonymous codon usage (RSCU) >1, thirty codons showed the codon usage bias in the chloroplast genes of all the three Alpinia species (Table S4).…”

Structural and Comparative Analysis of the Complete Chloroplast Genome of a Mangrove Plant: Scyphiphora hydrophyllacea Gaertn. f. and Related Rubiaceae Species

“…Among all the codons, leucine (Leu) was the most abundant amino acid with a frequency of 10.58%, followed by isoleucine (Ile) with a frequency of 8.61%, whereas cysteine (Cys) was less abundant with a frequency of 1.06% (Figure 3, Table S2 and S3). Leucine and isoleucine are among the more common codons in comparison with other previously reported land plant cp genomes [27,28]. All 19 A/U-ending codons had an RSCU value of >1, whereas two amino acids, methionine (Met) and tryptophan (Trp), with C/G-ending codons had RSCU values of <1 and showed no codon bias.…”

“…In the G. nanlingensis cp genome, there are two editing sites in the ndhB gene. At the same time, a notable RNA-editing event was also detected in all nine Rubiaceae species at the initiator codon (ACG), resulting in an ATG translational start codon in the ndhD gene, which is analogous to several other plants [27,33]. For the ycf 3 gene, one editing site is found in both Galium species, and no editing site was found in the other seven tested cp genomes.…”

“…Potential RNA-editing sites in S. hydrophyllacea plastome were analyzed using the PREP program, and the results showed that the most frequent conversions at the codon positions consist of serine (Ser) changing to leucine (Leu) ( Table 2). A total of 46 editing sites in 18 protein-coding genes were identified, with the ndhB and ndhD genes having the highest number of predicted RNA-editing sites, which is analogous to other land plants [27]. Furthermore, rpoB has four predicted RNA-editing sites, whereas accD, atpA, matK, and ndhA have three editing sites.…”

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…The plastomes of land plants have conserved structure but diversity prevails at the border position of LSC/SSC/IR of the genome. The size range of LSC, SSC and IR varies between the plastid genomes of species that advances to alterations in several genes and leads to the deletion of one copy of a gene or duplication of functional and non-functional genes of different sizes (Menezes et al, 2018; Saina et al, 2018). In the current study, all these ten Nicotiana species showed similarities with some variation as compared to the Nicotiana tabacum: in all these plants except Nicotiana tomentosiformis which have 60 bp in IRb region, the rps19 gene is present entirely in the LSC region but in Nicotiana tabacum rps19 gene extended 5bp in the IR region.…”