Chin Bull Bot ›› 2019, Vol. 54 ›› Issue (4): 441-454.doi: 10.11983/CBB18191

• RESEARCH ARTICLE • Previous Articles     Next Articles

Chloroplast Genome Structural Characteristics and Phylogenetic Relationships of Oleaceae

Zhao Yuemei1,Yang Zhenyan2,Zhao Yongping1,Li Xiaoling1,Zhao Zhixin1,Zhao Guifang3,*()   

  1. 1 College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, China
    2 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
    3 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
  • Received:2018-09-06 Accepted:2019-04-23 Online:2020-01-08 Published:2019-07-01
  • Contact: Zhao Guifang E-mail:gfzhao@nwu.edu.cn

Abstract:

In this study, the chloroplast genomes from 19 species (11 genera) in Oleaceae were compared to reveal the general characteristics and structural variations. The chloroplast genome sizes in Oleaceae were 154-165 kb, and the differences were mainly caused by the length of large single-copy regions. The chloroplast genome sizes of 3 species from the genus Jasminum differed greatly from that for other species; in addition, the introns from the clpP and accD genes were lost in Jasminum. Synteny analyses showed several gene rearrangements in 3 Jasminum species that were probably caused by inversions. The boundary genes between IRb/small single copy (SSC) and SSC/IRa regions in 3 Jasminum species differed from others. Repeat sequences and simple sequence repeat detection demonstrated that Jasminum had significant differences in repeat number and repeat length as compared with other genera. On the basis of shared protein-coding genes among 19 species, Abeliophyllum distichum and Forsythia suspensa were the early-diverging clades in Oleaceae.

Key words: Oleaceae, chloroplast genomes, structural characteristics, phylogeny

"

Table 2

Length of coding region and complete gene of intron-contained protein-coding genes of chloroplast genomes"

Species petD rps12 clpP rpoC1 rps16
1 483/1196 372/908 591/2047 2064/2821 267/1132
2 483/1218 372/908 591/2043 2073/2834 267/1147
3 483/1230 375/911 591/2045 2052/2820 267/1134
4 483/1261 381/917 591/2043 2073/2827 267/1153
5 483/1134 372/908 591/2045 2052/2811 255/1147
6 483/1148 372/908 591/2053 2073/2830 267/1136
7 483/1217 372/908 591/2039 2073/2834 267/1142
8 483/1196 372/908 588/2045 2064/2822 267/1131
9 483/1196 381/917 660 2076/2844 267/1162
10 483/1203 387/923 786 2052/2808 267/1154
11 483/1213 387/923 786 2052/2807 267/1161
12 483/1215 381/917 591/2041 2073/2833 267/1143
13 483/1217 372/908 591/2043 2073/2830 267/1143
14 483/1215 372/908 591/2046 2073/2832 267/1141
15 483/1213 371/907 591/2043 2073/2831 267/1142
16 483/1213 372/908 591/2044 2073/2831 267/1142
17 483/1215 373/909 591/2041 2073/2833 267/1141
18 483/1203 372/908 591/2047 2073/2834 267/1147
19 483/1199 372/913 591/2041 2073/2784 237/1115

Figure 1

The type and percentage of repeated sequences in the chloroplast genomes of 19 species in Oleaceae (A) Number of three type repeats; (B) Percentage of three type repeats; (C) Percentage of SSR types; (D) Number and types of SSRs"

Figure 2

Comparison of the border regions of the chloroplast genomes from 19 species in Oleaceae"

Figure 3

Graphic view of the alignment of chloroplast genomes from 19 species in Oleaceae The species number 1-19 same as Table 1. Sequence identity varying between 50% and 100% are drawn on the y axis of the plot, the x axis corresponds to the coordinates on the Abeliophyllum distichum chloroplast genome. Arrows indicate the annotated genes and their transcriptional direction."

Figure 4

Synteny analyses of chloroplast genomes from 19 species in Oleaceae The species number 1-19 same as Table 1."

Figure 5

Phylogenetic relationship of 19 species in Oleaceae inferred from ML and BI analyses based on shared protein-coding genes The numbers near each node are bootstrap support values in ML and posterior probability in BI. The outgroups are Cornus controversa, Echites umbellatus and Catharanthus roseus. ML: Maximum likelihood; BI: Bayesian inference"

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