Comparative Analyses on the Chloroplast Genome of Three Sympatric Atraphaxis Species

doi:10.11983/CBB22065

Abstract

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

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

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22065

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

Figures/Tables 12

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

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

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*

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

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

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

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.

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

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.

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.

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.

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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