Chloroplast genomes of Eriobotrya elliptica and an unknown wild loquat "YN-1"

Abstract

The chloroplast genomes of wild loquat can help to determine their place in the history of evolution. Here, we sequenced and assembled two novel wild loquat's chloroplast genomes, one is Eriobotrya elliptica, and the other is an unidentified wild loquat, which we named "YN-1". Their sizes are 159,471 bp and 159,399 bp, respectively. We also assembled a cultivated loquat named 'JFZ', its chloroplast genome size is 159,156 bp. A comparative study was conducted with six distinct species of loquats, including five wild loquats and one cultivated loquat. The results showed that both E. elliptica and "YN-1" have 127 genes, one gene more than E. fragrans, which is psbK. Regions trnF-GAA-ndhJ, petG-trnP-UGG, and rpl32-trnL-UAG were found to exhibit high variability. It was discovered that there was a positive selection on rpl22 and rps12. RNA editing analysis found several chilling stress-specific RNA editing sites, especially in rpl2 gene. Phylogenetic analysis results showed that "YN-1" is closely related to E. elliptica, E. obovata and E. henryi.

Keywords: Chloroplast genome; Phylogeny; RNA editing; Wild loquat.

Figure 1

Gene map of the Eriobotrya elliptica, “YN-1”, and “JFZ”. Thick lines indicate the extent of the inverted repeat regions (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counter clockwise. Different colors represent different functional groups of genes.

Figure 2

Comparison of gene number, gene type, and different region sizes of of different species of loquats.

Figure 3

Comparison of the borders of LSC, SSC, and IR regions of chloroplast genomes of different species of loquats.

Figure 4

Sliding window analysis (window length: 600 bp, step size: 200 bp) of the whole chloroplast genomes of six different kinds of loquat. X-axis, position of the mid point of a window; Y-axis, nucleotide diversity of each window.

Figure 5

Repeats (A) and SSRs (B) number comparison of six different species of loquats.

Figure 6

Chloroplast genome codon usage pattern related plot. (A) GC content of different codon sites. (B) Neutrality plot (GC12 against GC3). (C) The codon adaptation index (CAI) value of different function gene sets. (D) Relationship between GC3 and effective number of codons (ENC) (ENC-plot).

Figure 7

Phylogenetic tree, including 13 wild loquats, 1 cultivated loquat, Pyrus ussuriensis, Photinia lanuginosa. and Photinia prionophylla. The phylogenetic tree was constructed using whole chloroplast genome sequences of the 17 species of loquats (raxml-ng with parameters—model TVM+G—bs-trees 1000.).