3. Results
3.2 Characteristics of Primulina and Petrocodon plastomes
Sizes of the complete plastomes of the ten newly sequenced species ranged from 152323 bp (P. medica) to 153786 bp (P. cordata) (Table 3). Among these newly generated plastomes, the length of LSC ranging from 83218 bp (P. pengii) to 84890 bp (P. medica), the length of IRs ranging from 25415 bp (Pet. multiflorus) to 25495 bp (P.
pengii), and the length of SSC ranging from 16489 bp (P. medica) to 18279 bp (Pet.
multiflorus) (Table 3). The GC contents of assembled plastomes ranged from 37.5 –
37.6 % indicating the obviously AT-biased sequence content of the plastome which is consistent with most of the plant species (Shimada and Sugiura, 1991). However, the GC contents of IR are significantly higher than the values in SC regions (Fig. 5 and Table 3).
In the plastomes of Primulina and Petrocodon, no pseudogene, which is defined as genes possessing immature stop codon(s), was detected. The gene contents of the eight Primulina and two Petrocodon plastomes are identical. They harbor in total of 111 different genes, including 80 different protein coding genes, 27 different tRNA genes, and four different rRNA genes (Table 4). Among the 111 genes, 19 were completely duplicated in IR and three (rps19, ndhF and ycf1) were partially duplicated resulting from their locations on IR/SC boundaries. The trans-splicing genes, rps12, were partially duplicated with two of its exons located in IRs. Including those genes
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completely duplicated in IRs and excluding the incompletely duplicated parts of the IR boundaries located genes (but counting the trans-splicing gene, rps12, as two copies) the overall gene number of a Primulina or Petrocodon plastome is 131 with 87 protein coding genes, 36 tRNA genes and 8 rRNA genes (Table 4). There are 16 intron containing genes (not counting duplicated copy) in total with 11 protein coding genes and five tRNA genes (Table 4). Only the ycf3 and clpP gene contain two introns while the remaining genes contain one intron (Table 4). There are three pairs of genes overlapping with each other (psbD/psbC, ndhK/ndhC, atpE/aptB). The length of the coding regions (including RNA genes) accounts for 44.2 % of the total size of a Primulina or Petrocodon plastome in average, indicating the plastome structure of
species sequenced in this study is relatively compact comparing to the nucleus whose genome is usually dominated by non-coding sequences (Schmidt and Heslop-Harrison, 1998; Vicient et al., 1999; Meyers et al., 2001; Feschotte et al., 2002).
By comparing the gene contents of the two genera with the reference Bhcp genome and other Gesneriad plastomes, regardless of the annotation disparity which means the same gene was annotated into different names, there is no gene losses, relocations or structural inversions. This comparison suggest that plastomes of Gesneriaceae species sampled here are highly conserved in gene contents and gene orders.
Table 3. Plastome features of Gesneriaceae species.
Note: The unit of size and length of each plastomes is base pair (bp). The accession numbers of sequences from GenBank were shown in italic.
Scientific name Chinese name Voucher No./
Accession No.
cp size (GC %) LSC (GC %) SSC (GC %) IR (GC %)
Primulina lutea 黃花牛耳朵 KFC2916 153262 (37.6) 84094 (35.6) 18188 (31.2) 25490 (43.2)
Primulina pengii 彭氏報春苣苔 Peng24024 152354 (37.7) 83218 (35.7) 18146 (31.3) 25495 (43.2)
Primulina eburnea 牛耳朵 MF177038 152963 (37.6) 83934 (35.6) 18099 (31.1) 25465 (43.2)
Primulina longgangensis 弄崗唇柱苣苔 Peng22948 153191 (37.7) 84105 (35.6) 18168 (31.3) 25459 (43.2)
Primulina linearifolia 線葉唇柱苣苔 MF472013 153244 (37.6) 84149 (35.6) 18177 (31.2) 25459 (43.2)
Primulina liboensis 荔坡唇柱苣苔 MF177039 152989 (37.7) 84585 (35.6) 17478 (31.4) 25463 (43.2)
Primulina sclerophylla 硬葉唇柱苣苔 KFC2971 153185 (37.6) 84608 (35.6) 17641 (31.3) 25468 (43.2)
Primulina hezhouensis 賀州小花苣苔 KFC2914 153556 (37.6) 84757 (35.5) 17887 (31.3) 25456 (43.2)
Primulina huaijiensis 懷集報春苣苔 MF472012 153401 (37.6) 84334 (35.6) 18213 (31.2) 25427 (43.2)
Primulina medica 藥用唇柱苣苔 KFC2962 152323 (37.6) 84890 (35.5) 16489 (31.4) 25472 (43.2)
Primulina fimbrisepala 螞蝗七 KFC4144 153089 (37.5) 84684 (35.4) 17527 (31.2) 25439 (43.2)
Primulina cordata 心葉唇柱苣苔 KFC3021 153786 (37.5) 84789 (35.5) 18085 (31.2) 25456 (43.2)
Primulina brachytricha var. magnibracteata 短毛唇柱苣苔 MF177037 153723 (37.5) 84783 (35.4) 18078 (31.2) 25431 (43.2) Petrocodon coriaceifolius 革葉石山苣苔 KFC2943 153292 (37.5) 84345 (35.4) 18083 (31.2) 25432 (43.2)
Petrocodon multiflorus 多花石山苣苔 KFC2913 153227 (37.5) 84118 (35.4) 18279 (31.0) 25415 (43.2)
Lysionotus pauciflorus 吊石苣苔(石吊蘭) KX752081 153856 (37.5) 85087 (35.4) 17839 (31.2) 25465 (43.2)
Boea hygrometrica 旋朔苣苔 NC016468 153493 (37.6) 84701 (35.6) 17900 (31.0) 25446 (43.2)
Haberlea rhodopensis KX657870 153254 (37.7) 84299 (35.7) 17837 (31.7) 25559 (43.2)
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Fig. 5. The genome maps of Primulina and Petrocodon plastomes.
The genes drawn on inner side of the outer circle are transcribed clockwise, and those on the outer side are transcribed counterclockwise. IRs are shown in bold line in the outer circle. The inner circle indicates GC contents across the genome with lighter gray indicating AT contents. Genes belonging to different functional groups were shown in different colors.
Table 4. The gene contents of Primulina and Petrocodon plastomes.
Gene category Gene Name
Photosystem I psaA, psaB, psaC, psaI, psaJ
Photosystem II
psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
Cytochrome b/f complex petA, petB*, petD*, petG, petL, petN ATP synthase atpA, atpB, atpE, atpF*, atpH, atpI
NADH dehydrogenase
ndhA*, ndhB(×2)*, ndhC, ndhD, ndhE, ndhF#, ndhG, ndhH, ndhI, ndhJ, ndhK
RubisCO large subunit rbcL
RNA polymerase rpoA, rpoB, rpoC1*, rpoC2
Ribosomal proteins (SSU)
rps2, rps3, rps4, rps7(×2), rps8, rps11, rps12(×1.67)†*, rps14, rps15, rps16*, rps18, rps19#
Ribosomal proteins (LSU) rpl2(×2)*, rpl14, rpl16, rpl20, rpl22, rpl23(×2), rpl32, rpl33, rpl36 Protease, Maturase clpP**, matK
trnA-UGC(×2)*, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-UCC, trnH-GUG, trnI-CAU(×2), trnI-GAU(×2)*, trnK-UUU*, trnL-CAA(×2), trnL-UAA*, trnL-UAG, trnM-CAU, trnfM-CAU, trnN-GUU(×2), trnP-UGG, trnQ-UUG, trnR-ACG(×2), trnR-UCU, trnS-GCU(×2), trnS-UGA, trnT-GGU(×2), trnV-GAC(×2), trnV-UAC*, trnW-CCA, trnY-GUA
Ribosomal RNAs (rRNA) rrn4.5(×2), rrn5(×2), rrn16(×2), rrn2(×2) (×2): Genes duplicated in IRs.
*Genes with one intron.
**Genes with two introns.
† The trans-splicing gene, rps12, which possesses three exons with two of which duplicated in IRs.
Therefore, the gene was marked as ×1.67 copies.
# The partially duplicated genes locating on the IR/SC boundary.
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