Chloroplast Genome Structural Characteristics and Phylogenetic Relationships of Oleaceae

doi:10.11983/CBB18191

Abstract

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

Yuemei Zhao,Zhenyan Yang,Yongping Zhao,Xiaoling Li,Zhixin Zhao,Guifang Zhao. Chloroplast Genome Structural Characteristics and Phylogenetic Relationships of Oleaceae[J]. Chinese Bulletin of Botany, 2019, 54(4): 441-454.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB18191

https://www.chinbullbotany.com/EN/Y2019/V54/I4/441

Figures/Tables 7

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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