同域分布的3种木蓼属植物叶绿体基因组比较

doi:10.11983/CBB22065

摘要/Abstract

摘要： 刺木蓼(Atraphaxis spinosa)、额河木蓼(A. jrtyschensis)和细枝木蓼(A. decipiens)是同域分布在我国新疆北部的3种木蓼属物种。通过二代高通量测序, 对叶绿体基因组进行组装和注释, 比较3个物种的叶绿体基因组差异并进行系统发育分析。结果表明, 木蓼属3个物种的叶绿体全基因组大小为164 106-164 216 bp, 与其它绿色植物类似, 由1个大单拷贝区(LSC)、1个小单拷贝区(SSC)及介于二者之间的2个反向重复区(IRa/IRb)组成。在刺木蓼、额河木蓼和细枝木蓼中检测到48-49个串联重复序列及59-63个简单重复序列(SSR)。3个物种的核苷酸多样性平均值为0.000 96, K_a/K_s平均值为0.030 3, 遗传距离平均值为0.001 0。通过对3个物种的叶绿体基因组进行比较, 发现编码区比非编码区更保守。系统发育分析结果显示3个物种的亲缘关系较近。该研究基于叶绿体基因组对木蓼属物种的亲缘关系进行分析, 揭示了3个同域分布的物种之间的亲缘关系以及木蓼属在蓼科中的系统位置。研究结果可为木蓼属的分类学、系统学和生物地理学研究提供参考。

关键词: 叶绿体基因组, 木蓼属, 同域分布, 比较基因组学, 系统发育

Abstract: Atraphaxis spinosa, A. jrtyschensis, and A. decipiens are three species with sympatric distribution in northern Xinjiang, China. In this study, their chloroplast genomes were assembled and annotated with the second-generation high-throughput sequencing technology (NGS). We compared the nucleotide sequences of the chloroplast (cp) genomes of these three Atraphaxis species and carried out the phylogenetic analysis. The results showed that the cp genomes of the three species ranged from 164 106 bp to 164 216 bp, similar to that of other green plants, all including a pair of inverted repeats separated by a large single-copy and a small single-copy region. We detected a total of 48-49 tandem repeats and 59-63 simple sequence repeats (SSRs) from the three cp genomes. The mean value of nucleotide diversity of the three species was 0.000 96, the average score of K_a/K_s ratio was 0.030 3, and the mean genetic distance value was 0.001 0. A comparative analysis showed that the coding regions were more conserved than the non-coding regions. The phylogenetic analysis showed that the three species were closely related. This study reveals the phylogenetic relationships among the three sympatric distribution species of Atraphaxis based on complete chloroplast genomes, and the phylogenetic position of Atraphaxis in the family Polygonaceae. This work may provide a reference for taxonomic, systematic and biogeographical studies of Atraphaxis.

Key words: chloroplast genome, Atraphaxis, sympatric distribution, comparative genomics, phylogeny

褚振州, 古丽巴哈尔·依斯拉木, 屈泽众, 田新民. 同域分布的3种木蓼属植物叶绿体基因组比较. 植物学报, 2023, 58(3): 417-432.

Zhenzhou Chu, Gulbar Yisilam, Zezhong Qu, Xinmin Tian. Comparative Analyses on the Chloroplast Genome of Three Sympatric Atraphaxis Species. Chinese Bulletin of Botany, 2023, 58(3): 417-432.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB22065

https://www.chinbullbotany.com/CN/Y2023/V58/I3/417

图/表 12

图1 木蓼属3个物种的叶绿体基因组标注在大环外部的基因按照顺时针方向转录, 标注在大环内部的基因按照逆时针方向转录。不同基因功能标注不同颜色; 内环阴影部分代表3个物种叶绿体基因组的GC组成。LSC: 大单拷贝区; SSC: 小单拷贝区; IR: 反向重复区。* 含有内含子的基因

Figure 1 The chloroplast genome of the three Atraphaxis species Genes on the outside of the large circle are transcribed clockwise and those on the inside are transcribed counterclockwise. The genes are color-coded based on their function. The dashed area represents the GC composition of the chloroplast genome. LSC: Large single copy region; SSC: Small single copy region; IR: Inverted repeat region. * Genes including introns

表1 木蓼属3个物种的叶绿体基因组基本信息

Table 1 Basic information on the chloroplast genome of the three Atraphaxis species

	Atraphaxis spinosa	A. jrtyschensis	A. decipiens
Gene size (bp)	164106	164216	164187
LSC (bp)	88812	88900	88870
SSC (bp)	13456	13485	13485
IR (bp)	30919	30916	30916
No. of genes	133	133	133
No. of PCGs	88	88	88
No. of tRNA	37	37	37
No. of rRNA	8	8	8
No. of duplicated genes	20	20	20
GC content (%)	37.4	37.5	37.5

表2 木蓼属3个物种叶绿体基因组的基因注释信息

Table 2 Gene annotation in the chloroplast genome of the three Atraphaxis species

Gene category	Group of genes	Name of genes
Self-replication	Ribosomal RNAs	rrn4.5#, rrn5#, rrn16#, rrn23#
	Transfer RNAs	trnV-GAC#, trnl-GAU#, trnA-UGC#, trnR-ACG#, trnN- GUU#, trnL-CAA#, trnl-CAU#, trnH-GUG, trnK-UUU, trnQ-UUG, trnS-GUC, trnG-UCC*, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE-UUC, trnT-GGU, trnS-UGA, trnG-GCC, trnfM-CAU, trnS-GGA, trnT-UGU, trnL-UAA*, trnF-GAA, trnM-CAU, trnV-UAC*, trnW-CCA, trnP-UGG*
Gene for photosynthesis	Small subunit of ribosomal proteins (SSU)	rps19, rps7#, rps12#, rps15, rps2, rps14, rps4, rps18, rps3, rps11, rps16**
	Large subunit of ribosomal proteins (LSU)	rpl2#, rpl23#, rpl32, rpl33, rpl20, rpl14, rpl16*, rpl36, rpl22*
	RNA polymerase	rpoC2, rpoC1, rpoB, rpoA*
	Photosystem I	psaC, psaA, psaB, psaJ, psaI
	Photosystem II	psbK, psbI, psbM, psbD, psbC, psbZ, psbJ, psbL, psbF, psbE, psbB, psbT, psbH, psbA, psbN
Other genes	Subunits of cytochrome b/f complex	petN, petA, petL, petG, petB, petD**
	Protease	clpP**
	Subunits of ATP synthase	atpA, atpF, atpH, atpI, atpE, atpB*
	Large subunit of Rubisco	rbcL
	Subunits of NADH-dehydrogenase	ndhB#, ndhF, ndhD, ndhC, ndhE, ndhG, ndhI, ndhA*, ndhH, ndhJ, ndhK, ndhC*
	Maturase	matK
	Envelop membrane protein	cemA
	Subunit of acetyl-CoA-carboxylase	accD
	C-type cytochrome synthesis gene	ccsA
	Translational initiation factor	infA
Gene of unknown function	Hypothetical chloroplast reading frames (ycf)	ycf1#, ycf2#, ycf3*, ycf4, ycf15*

图2 木蓼属3个物种叶绿体基因组中的重复序列分析 (A) 正向重复、反向重复和回文重复的总数; (B) 正向重复序列的数量; (C) 回文重复序列的数量; (D) 反向重复序列的数量

Figure 2 Analysis of the repeat sequences in the chloroplast genome of the three Atraphaxis species (A) Total number of the forward repeats, reverse repeats and palindromic repeats; (B) Number of the forward repeats; (C) Number of the palindromic repeats; (D) Number of the reverse repeats

图3 木蓼属3个物种叶绿体基因组中的简单重复序列(SSRs) (A) 不同类型SSR的分布; (B) 不同类型SSR的频率

Figure 3 Simple sequence repeats (SSRs) in the chloroplast genome of the three Atraphaxis species (A) Distribution of different SSR types; (B) Frequency of different type of SSRs

图4 木蓼属3个物种的叶绿体基因组密码子使用偏好性每个氨基酸的3个柱形从左到右依次为刺木蓼(Atraphaxis spinosa)、额河木蓼(A. jrtyschensis)和细枝木蓼(A. decipiens)。RSCU: 相对同义密码子使用度

Figure 4 The codon usage bias of the chloroplast genomes in the three Atraphaxis species Columns above each amino acid from left to right are A. spinosa, A. jrtyschensis and A. decipiens, respectively. RSCU: Relative synonymous codon usage

图5 木蓼属3个物种的叶绿体基因组核苷酸多样性 LSC、SSC和IR同图1。

Figure 5 The nucleotide diversity of the chloroplast genomes of the three Atraphaxis species LSC, SSC and IR are the same as shown in Figure 1.

图6 木蓼属3个物种中80个蛋白质编码基因的非同义替换/同义替换(Ka/Ks)比值 (A) 刺木蓼vs额河木蓼; (B) 刺木蓼vs细枝木蓼

Figure 6 The non-synonymous-to-synonymous substitution (Ka/Ks) ratios of 80 protein-coding genes among the three Atraphaxis species (A) A. spinosa vs A. jrtyschensis; (B) A. spinosa vs A. decipiens

图7 蓼科7个物种之间的LSC、SSC和IR区域的边界位置比较 LSC、SSC和IR同图1。JLB: LSC与IRb的边界; JSB: IRb与SSC的边界; JSA: SSC与IRa的边界; JLA: IRa与LSC的边界。

Figure 7 Comparison of the border positions of LSC, SSC, and IR regions among the seven species of the Polygonaceae LSC, SSC and IR are the same as shown in Figure 1. JLB: Junction line between LSC and IRb; JSB: Junction line between IRb and SSC; JSA: Junction line between SSC and IRa; JLA: Junction line between IRa and LSC.

图8 7种蓼科植物叶绿体基因组mVISTA序列分析灰线表示基因方向及在LSC、SSC和IR区域的位置。序列一致性在y轴上显示为50%-100%的百分比。基因组不同区域用不同颜色区分。

Figure 8 mVISTA sequence analysis on the chloroplast genome among seven species of the Polygonaceae The gray lines show the gene orientation and the position in the LSC, SSC, and IR regions. Sequence identity is shown as a percentage between 50%-100% on y-axis. Genome regions are distinguished by different colors.

图9 基于叶绿体基因组中蛋白编码序列构建的37个蓼科物种的系统发育树 (A) 基于贝叶斯法(BI)构建的系统发育树, 分支上的数值为后验概率; (B) 基于最大似然法(ML)构建的系统发育树, 分支上的数值为自举值。以黄花补血草为外类群。红色代表本研究的3个物种。紫色代表蓼族(Trib. Polygoneae)的物种, 绿色代表木蓼族(Trib. Atraphaxideae)的物种。

Figure 9 Phylogenetic tree of 37 species in the Polygonaceae based on the protein coding sequences in their chloroplast genomes (A) The Bayesian inference (BI) tree with posterior probabilities values on the branches; (B) Maximum likelihood (ML) tree with bootstrap values on the branches. Limonium aureum is used as outgroup. The red color represents the three species in this study. The purple color represents the species of Trib. Polygoneae, and the green color represents the species of Trib. Atraphaxideae.

图10 基于贝叶斯法(BI), 利用ycf1、ndhA、atpA和atpI高变异位点联合构建的36个蓼科物种的系统发育树以黄花补血草作为外类群。

Figure 10 Phylogenetic tree of 36 species in the Polygonaceae based on Bayesian inference (BI) with a combination of high variance loci of ycf1, ndhA, atpA and atpI Limonium aureum is used as outgroup.

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