Evolutionary Analysis of Chloroplast Genome of Parnassia

doi:10.7525/j.issn.1673-5102.2022.04.012

Abstract

Abstract:

Sequence variation and gene composition of chloroplast genome could effectively reflect the phylogenetic and evolutionary relationships among plants. In this study， DNA libraries were prepared and sequenced by the Illumina HiSeq， chloroplast genomes offive species of Parnassia and allied genera were assembled respectively， and the structural characteristics， sequence genetic variation and codon preference of protein coding genes of Parnassia chloroplast genome with related species were compared and analyzed. The results showed that the chloroplast genome of Parnassia was conserved tetrad structure， and pseudogenization of several genes were found in P. palustris， but the chloroplast gene composition of other species was the same， encoding 115 genes. Compared with the relative species， the intron of rpl16 gene were lost in all species of Parnassia. The ratio of nonsynonymous/synonymous substitution rate of protein coding genes was low， and chloroplast genes might experience purification selection. Codon preference was consistent with the phylogenetic relationship shown by protein coding sequences. This study reveals that selection pressure may play an important role in the evolution of protein-coding genes in the chloroplast genome of Parnassia， which could enhance the understanding about evolution and adaptation of this genus.

Key words: Parnassia, plastome, codon usage bias, phylogeny, evolution

CLC Number:

Q685.17

Mingze XIA, Faqi ZHANG, Xiaofeng CHI, Shuang HAN, Shilong CHEN. Evolutionary Analysis of Chloroplast Genome of Parnassia[J]. Bulletin of Botanical Research, 2022, 42(4): 626-636.

Figures/Tables 10

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物种 Species	长度 Length /bp				基因数量 Number of gene				GenBank号 GenBank number
物种 Species	LSC	SSC	IR	叶绿体基因组 plastome	tRNA	rRNA	蛋白编码基因 Protein-coding gene	总数 Total	GenBank号 GenBank number
鸡肫梅花草Parnassia wightiana	82 501	18 903	25 150	151 704	37（30）	8（4）	90（81）	135（115）	MK887922
三脉梅花草Parnassia trinervis	84 137	18 289	25 582	153 590	37（30）	8（4）	90（81）	135（115）	MH544205^*
青铜钱Parnassia tenella	82 892	18 728	25 206	152 032	37（30）	8（4）	90（81）	135（115）	MK887920^*
梅花草Parnassia palustris	82 175	14 741	25 892	148 700	37（30）	8（4）	79（70）	124（104）	NC045280
甘肃梅花草Parnassia gansuensis	82 920	18 572	25 433	152 358	37（30）	8（4）	90（81）	135（115）	MZ508382
白耳菜Parnassia foliosa	81 723	18 977	25 278	151 256	37（30）	8（4）	90（81）	135（115）	MZ508380
德格梅花草Parnassia degeensis	83 007	18 704	25 225	152 161	37（30）	8（4）	90（81）	135（115）	MK887920
永瓣藤Monimopetalum chinense	87 461	18 606	26 560^**	159 208	38（30）	8（4）	87（80）	133（114）	MK450440
双花假卫茅Microtropis biflora	86 107	18 056	25 662	155 487	37（30）	8（4）	85（79）	130（113）	MZ905494^*
华北卫茅Euonymus maackii	86 485	18 339	26 345	157 514	37（30）	8（4）	87（80）	132（114）	MZ905495^*
圆叶南蛇藤Celastrus kusanoi	84 920	18 331	26 603	156 457	37（30）	8（4）	88（80）	133（114）	MZ905493^*

基因 Gene	鸡肫梅花草 P. wightiana	三脉梅花草 P. trinervis	青铜钱 P. tenella	梅花草 P. palustris	甘肃梅花草 P. gansuensis	白耳菜 P.foliosa	德格梅花草 P. degeensis	永瓣藤 M.chinense	双花假卫茅 M. biflora	华北卫茅 E. maackii	圆叶南蛇藤 C. kusanoi
rps12	372/537	372/537	372/537	372/537	372/537	372/537	372/537	372/543	372/526	372/544	372/543
trnK-UUU	72/2527	72/2569	72/2530	72/2523	72/2529	72/2560	72/2530	72/2489	72/2500	72/2506	72/2462
rps16	291/—	291/—	291/—	291/—	291/—	291/—	291/—	297/—	267/852	297/—	291/—
trnG-UCC	71/857	71/895	71/844	71/785	71/846	71/837	71/836	71/834	71/668	71/782	71/755
atpF	555/755	555/759	555/747	555/772	555/762	555/746	555/753	555/721	555/710	555/705	555/681
rpoC1	2031/788	2031/781	2052/779	2031/789	2031/781	2031/810	2031/779	2049/838	2043/761	2049/849	2049/813
ycf3	507/1536	507/1552	507/1509	507/1546	507/1520	507/1543	507/1508	507/1492	507/1453	513/1489	507/1458
trnL-UAA	85/605	85/606	85/607	85/616	85/607	85/596	85/606	85/535	85/502	94/575	85/534
trnV-UAC	76/261	76/677	76/272	76/699	76/273	76/668	76/273	76/659	75/584	76/748	76/658
clpP	591/1539	591/1535	591/1520	591/1523	591/1520	591/1546	591/1513	591/1497	588/1449	591/1481	591/1493
petB	648/816	648/801	648/806	648/816	648/810	648/807	648/805	648/771	648/782	648/778	648/745
petD	483/803	483/823	483/798	483/790	483/803	483/807	483/798	483/757	483/724	483/723	483/767
rpl16	441/—	441/—	441/—	441/—	441/—	441/—	441/—	408/1141	408/1004	408/1126	408/1092
rpl2	825/683	825/683	825/683	825/683	825/683	825/683	825/683	825/685	816/659	825/679	825/685
ndhB	1479/683	1479/679	1479/679	1479/679	1479/679	1479/679	1479/679	1479/678	1479/684	1479/685	1479/685
trnI-GAU	72/950	72/950	72/949	72/950	72/950	72/950	72/949	72/957	72/941	72/949	72/948
trnA-UGC	73/804	73/804	73/798	73/804	73/804	73/804	73/798	73/799	73/808	73/799	73/798
ndhA	1092/1117	1092/1183	1092/1164	—/—	1092/1150	1092/1153	1092/1166	1092/1169	1092/1078	1092/1178	1092/1185

物种 Species	GC /%	GC1 /%	GC2 /%	GC3 /%	T3s	C3s	A3s	G3s	CAI	ENc	GC3s
鸡肫梅花草P. wightiana	39.27	48.57	39.91	29.33	0.4694	0.1681	0.4225	0.171	0.171	49.28	0.264
三脉梅花草P. trinervis	39.30	48.55	39.97	29.39	0.4694	0.1681	0.4213	0.172	0.171	49.33	0.265
青铜钱P. tenella	39.27	48.54	39.94	29.34	0.4701	0.1675	0.4217	0.172	0.172	49.20	0.264
梅花草P. palustris	39.16	48.41	39.93	29.15	0.4707	0.1678	0.4238	0.169	0.171	49.16	0.262
甘肃梅花草P. gansuensis	39.30	48.56	39.92	29.42	0.4689	0.1691	0.4222	0.171	0.171	49.32	0.265
白耳菜P. foliosa	39.21	48.51	39.83	29.30	0.4700	0.1675	0.4226	0.171	0.170	49.27	0.264
德格梅花草P. degeensis	39.29	48.58	39.92	29.36	0.4701	0.1679	0.4216	0.172	0.172	49.22	0.265
永瓣藤M. chinense	39.52	48.75	40.00	29.80	0.4660	0.1711	0.4195	0.174	0.173	49.70	0.269
双花假卫茅M. biflora	39.21	48.76	39.90	28.97	0.4718	0.1652	0.4259	0.168	0.172	49.02	0.260
华北卫茅E. maackii	39.52	48.73	39.88	29.95	0.4666	0.1730	0.4178	0.174	0.175	49.74	0.271
圆叶南蛇藤C. kusanoi	39.38	48.62	39.86	29.66	0.4689	0.1717	0.4194	0.171	0.174	49.50	0.267

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