Analysis of the Chloroplast Genome Characteristics of 6 Species of Yucca

doi:10.7525/j.issn.1673-5102.2023.01.012

Abstract

Abstract:

In order to clarify the characteristics and sequences variation of the chloroplast genomeof Yucca， a comparative genomics of the chloroplasts was performed， and a phylogenetic tree based on the chloroplast genome was constructed. The chloroplast genome of Y. treculeana was obtained by high-throughput sequencing technology， and combined with the published chloroplast genome of Yucca， the chloroplast genomes of six species of Yucca were studied by comparative genomics， including basic structure， SSR， boundary contraction and expansion， sequence variation and phylogenetic analysis respectively. The results showed that the chloroplast genome size， gene type and number of the six Yucca species were similar， and the interspecific genome structure was conserved. Several repeated sequences were detected in the chloroplast genome of Yucca， among which SSR loci were mostly composed of mononucleotide， dinucleotide and tetranucleotide， and preferred A and T bases. Three regions with high variation（psbK-psbl-trnS-GCU， rpl20-rps12 and ccsA-ndhD） were identified from the chloroplast genomes of six Yucca species according to the nucleic acid polymorphism index（π）≥0.008. The phylogenetic relationships constructed from the chloroplast genome and LSC+SSC region sequences were basically consistent， and the phylogenetic relationships among six Yucca species were confirmed， among which Y. treculeana and Y. queretaroensis were most closely related. The sequencing obtained Y. treculeana chloroplast genome， revealed the genome characteristics and sequence variation of six Yucca species， and clarified the relatedness among various species. The results could provide reference for subsequent molecular marker development and phylogenetic research.

Key words: Yucca, chloroplast genome, structural characteristics, locus of variation, phylogenetic analysis

CLC Number:

S563.8

Fei WANG, Wenzhi ZHAO, Zhanghong DONG, Luyao MA, Weiying LI, Zongyan LI, Peiyao XIN. Analysis of the Chloroplast Genome Characteristics of 6 Species of Yucca[J]. Bulletin of Botanical Research, 2023, 43(1): 109-119.

Figures/Tables 9

Fig.1

Table 1

Table 2

Chloroplast genome gene types of six Yucca species

基因功能分类

Gene function

classification

基因分组

Group of genes

基因列表

Gene list

自我复制相关基因

Self-replication

核糖体RNA基因

rRNA genes

rrn16²、rrn23²、rrn4.5²、rrn5²

转运RNA基因

tRNA genes

trnK-UUU（2）、trnQ-UUG、trnS-GCU、trnG-GCC（2）、trnR-UCU、trnC-GCA、trnD-GUC、trnY-GUA、trnE-UUC、trnT-GGU、trnS-UGA、trnG-UCC、trnfM-CAU、trnS-GGA、trnT-UGU、trnL-UAA（2）、trnF-GAA、trnV-UAC（2）、trnM-CAU、trnW-CCA、trnP-UGG、trnL-UAG、trnN-GUU²、trnR-ACG²、trnA-UGC²（2）、trnI-GAU²（2）、trnV-GAC²、trnL-CAA²、trnI-CAU²、trnH-GUG²

核糖体小亚基

Small subunit of ribosome

rps16（2）、rps2、rps14、rps4、rps18、rps12²（3）、rps11、rps8、rps3、rps19²、rps7²、rps15

核糖体大亚基

Large subunit of ribosome

rpl33、rpl20、rpl36、rpl14、rpl16（2）、rpl22、rpl2²（2）、rpl23²、rpl32（Ysⁿ）

RNA聚合酶亚基

RNA polymerase

rpoC2、rpoC1（2）、rpoB、rpoA

光合作用相关基因

Genes for

photosynthesis

NADH脱氢酶

NADH dehydrogenase

ndhJ、ndhK、ndhC、ndhB²（2）、ndhF、ndhD、ndhE、ndhG、ndhI、ndhA（2）、ndhH

ATP合成酶

ATP synthase

atpA、atpF（2）、atpH、atpI、atpE、atpB

光合系统Ⅰ基因

Photosystem I gene

psaB、psaA、psaI、psaJ、psaC

光合系统Ⅱ基因

Photosystem II gene

psbA、psbK、psbI、psbM、psbD、psbC、psbZ、psbJ、psbL、psbF、psbE、

psbB、psbT、psbN、psbH

细胞色素b/f复合体基因

Cytochrome b/f complex

petN、petA、petL、petG、petB（2）、petD（2）

RubisCO大亚基

RubisCO large subunit

rbcL

其他基因

Other genes

成熟酶K基因

Maturase K gene

matK

蛋白酶基因

Protease gene

clpP（3）

囊膜蛋白基因

Envelop membrane protein

cemA

C型细胞色素合成基因

C-type cytochrome synthesis

ccsA

乙酰辅酶A羧化酶亚基

Acetyl-CoA carboxylase beta subunit

accD

未知功能基因

Unknown function genes

假定叶绿体阅读框

Hypothetical chloroplast reading frames

ycf4、ycf2²、ycf1、ycf3（3）

Table 2

Fig.2

Fig.3

Fig.4

Fig.5

Fig.6

Fig.7

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物种 Species	登录号 GenBank	基因组大小 Genome size/bp	LSC区长 Length /bp	SSC区长 Length /bp	IR区长 Length /bp	总基因数 Total genes	总GC含量 Content GC /%	蛋白编码基因 Protein coding	tRNA	rRNA
无刺龙舌兰 Y. treculeana	OL912952	157 579	85 940	18 279	26 680	131	37.8	85	38	8
西地格丝兰 Y. schidigera	KX931469	156 158	86 107	16 635	26 708	130	37.9	84	38	8
柔软丝兰 Y. filamentosa	KX931467	157 785	86 135	18 292	26 679	131	37.8	85	38	8
克雷塔罗丝兰 Y. queretaroensis	KX931468	157 814	86 146	18 294	26 687	131	37.8	85	38	8
短叶丝兰 Y. brevifolia	MW281836	158 016	86 313	18 299	26 702	131	37.8	85	38	8
Y. jaegeriana	MW281848	158 020	86 314	18 302	26 702	131	37.8	85	38	8

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