Phylogenetic analysis of Sorbus ser. Folgnerianae (Rosaceae)

doi:10.12302/j.issn.1000-2006.202205003

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (4): 25-36.doi: 10.12302/j.issn.1000-2006.202205003

Special Issue: 专题报道Ⅰ：郑万钧先生诞辰120周年纪念专题Ⅱ

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Phylogenetic analysis of Sorbus ser. Folgnerianae (Rosaceae)

MA Jianhui(), CHEN Xin^*(), GENG Liyang, TANG Chenqian, WEI Xueyan

Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China

Received:2022-05-02 Revised:2022-06-10 Online:2024-07-30 Published:2024-08-05
Contact: CHEN Xin E-mail:2556429572@qq.com;chenxinzhou@njfu.edu.cn

Abstract

Abstract:

【Objective】To test whether Sorbus ser. Folgnerianae is a monophyletic group and to reconstruct the phylogenetic relationship among three species, S. dunnii, S. folgneri and S. hemsleyi.【Method】Morphological characteristics of leaves, flowers and fruits of Ser. Folgnerianae species were compared through specimen examination and field observation. Phylogenetic relationships within Ser. Folgnerianae were analyzed based on the comparison of the plastid genomes, repeat sequences, sequence variations of the five plastid genomes newly sequenced including three Ser. Folgnerianae species and S. megalocarpa from Sect. Aria, together with other plastid genomes available in this genus, using representatives of related genera in Rosaceae and Barbeya oleoides (Barbeyaceae) as the outgroups.【Result】Species of Ser. Folgnerianae can be easily distinguished from each other in the number of styles, color of anthers, fruit morphology and the persistence of calyx. Plastid genomes of five samples have a similar structure, gene content and organization. This sizes of plastid genomes range from 159 898 to 160 755 bp, with the GC contain range between 36.4% and 36.6%. All plastid genomes contain 113 unique genes (79 protein-coding genes, 30 tRNA genes and four ribosomal RNA genes). The IR region has two pseudogenes, rps19^Ψand ycf1^Ψ, with different extension lengths. 48-54 simple sequence repeats (SSRs), 36-49 long repeats sequences (LRSs) and 20 highly variable regions in the noncoding regions are identified as the most promising potentially variable makers for population genetics, species delimitation and phylogenetic studies. Phylogenetic analyses under ML/BI indicated that Sorbus is polyphyletic and the six sections within it are all monophyletic. Although, three sampled species of Ser. Folgnerianae are clustered in one group, S. Alnifolia of Ser. Alnifolia is more closely related to S. dunnii and S. folgneri than S. hemsleyi.【Conclusion】Sorbus ser. Folgnerianae is not monophyletic. Morphological characteristics and plastid genome analysis are effective in understanding the phylogenetic relationship in Ser. Folgnerianae.

Key words: Sorbus, morphology, plastid genome, phylogeny

CLC Number:

S718.4

MA Jianhui, CHEN Xin, GENG Liyang, TANG Chenqian, WEI Xueyan. Phylogenetic analysis of Sorbus ser. Folgnerianae (Rosaceae)[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2024, 48(4): 25-36.

Figures/Tables 9

Table 1

Fig. 1

Fig. 2

Table 2

Table 3

Plastid genome gene content and functional classification in three Sorbus ser. Folgnerianae species and S. megalocarpa"

基因功能 function	基因分类 gene type	基因名称 gene	基因数量 number of genes
自我复制 self replication	rRNA	rrn4.5^a、rrn5^a、rrn16^a、rrn23^a	4
	tRNA	trnA-UGC^a、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、 trnfM-CAU、trnG-UCC^、trnG-GCC、trnH-GUG、trnI-CAU^a、 trnI-GAU^a、trnK-UUU^、trnL-CAA^a、trnL-UAA^、trnL-UAG、 trnM-CAU、trnN-GUU^a、trnP-UGG、trnQ-UUG、trnR-ACG^a、 trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、 trnV-GAC^a、trnV-UAC^、trnW-CCA、trnY-GUA	30
	核糖体小亚基 ribosomal proteins(SSU)	rps2、rps3、rps4、rps7^a、rps8、rps11、rps12^a、 rps14、rps15、rps16^、rps18、rps19/rps1 $9 Ψ a$	12
	核糖体大亚基 ribosomal proteins(LSU)	rpl2^a、rpl14、rpl16^、rpl20、rpl22、 rpl23^a、rpl32、rpl33、rpl36	9
	RNA聚合酶亚基 RNA polymerase	rpoA、rpoB、rpoC1^、rpoC2*	4
光合作用 genes for photosynthesis	光合系统Ⅰ photosystemⅠ	psaA、psaB、psaC、psaI、psaJ,	5
	光合系统Ⅱ photosystemⅡ	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、 psbJ、psbK、psbL、psbM、psbN、psbT、psbZ	15
	细胞色素复合物 cytochrome b/f complex	petA、petB^、petD^、petG、petL、petN	6
	ATP合成酶 ATP synthase	atpA、atpB、atpE、atpF^、atpH、atpI*	6
	NADH脱氢酶 subunits of NADH-dehydrogenase	ndhA^、ndhB^a、ndhC、ndhD、ndhE、 ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK	11
	二磷酸核酮糖羧化酶大亚基 rubiscoCO large subunit	rbcL	1
其他基因 hypothetical chloroplast reading frames	乙酰 CoA 羧化酶 subunit of Acetyl-CoA-carboxylase	accD	1
	膜包被蛋白基因 envelop membrane protein gene	cemA	1
	c型细胞色素合成基因 c-type cytochrom synthesis gene	ccsA	1
	蛋白酶基因 protease gene	clpP^**	1
	成熟酶基因 maturase gene	matK	1
	翻译起始因子 translation initiation factor	infA	1
未知功能 unknow function	假定的质体读码框 hypothetical chloroplast reading frames	ycf1/ycf $1 Ψ a$ 、ycf2^a、ycf3^*、ycf4*	4

Table 3

Fig. 3

Fig. 4

Fig. 5

Fig. 6

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种名species	采集地 location	地理坐标 geographical coordinates	海拔/m altitude	采集时间 (年-月-日) collection time (year-month-day)	采集人及凭证标本 collector and voucher	GenBank登录号 GenBank accession number
棕脉花楸 S. dunnii	安徽黄山	118°10'15.96″E, 30°6'58.38″N	1 186	2019-05-20	陈昕、李嘉宝,1430	OK054488
石灰花楸 S. folgneri	湖北兴山	110°29'46.97″E, 31°19' 05.16″N	1 789	2016-05-24	陈昕、洑香香、刘清亮,0506	ON262428
石灰花楸 S. folgneri	四川都江堰	103°19'45.68″E, 29°32'50.47″N	1 163	2021-04-23	朱大海,2000	ON262429
江南花楸 S. hemsleyi	湖北神农架	110°18'30.14″E, 31°35'55.67″N	1 830	2016-05-25	陈昕、洑香香、刘清亮,0522	OQ100083
大果花楸 S. megalocarpa	四川龙苍沟	102°53'13.75″E, 29°37'48.37″N	1 358	2021-03-21	胡太伦,1992	ON259046

样本 sample	大小/bp plastome length	大单拷贝区长度/ bp LSC length	小单拷贝区长度/ bp SSC length	反向区长度/bp IR length	编码区长度/% coding regions length	非编码区长度/% noncoding regions length	GC含量/% GC content							unique 基因数 unique genes	unique 蛋白编码基因数 unique CDS	tRNA 总数 total tRNA	rRNA 总数 total rRNA		基因总数 total genes
样本 sample	大小/bp plastome length	大单拷贝区长度/ bp LSC length	小单拷贝区长度/ bp SSC length	反向区长度/bp IR length	编码区长度/% coding regions length	非编码区长度/% noncoding regions length	总计 total	LSC	SSC	IR	CDS	rRNA	tRNA	unique 基因数 unique genes	unique 蛋白编码基因数 unique CDS	tRNA 总数 total tRNA	rRNA 总数 total rRNA		基因总数 total genes
棕脉花楸 S. dunnii	160 280	88 053	19 409	26 409	56.43	43.57	36.5	34.2	30.3	42.6	37.7	55.6	53.3	113	79	30		4		132
石灰花楸 S. folgneri (ON262428)	160 631	88 333	19 480	26 409	56.32	43.68	36.4	34.1	30.2	42.6	37.7	55.6	53.3	113	79	30		4		132
石灰花楸 S. folgneri (ON262429)	160 755	88 483	19 454	26 409	56.26	43.74	36.4	34.1	30.3	42.6	37.7	55.6	53.3	113	79	30		4		132
江南花楸 S. hemsleyi	160 527	88 415	19 304	26 404	56.34	43.66	36.4	34.1	30.3	42.7	37.7	55.6	53.3	113	79	30		4		132
大果花楸 S. megalocarpa	159 868	87 713	19 335	26 410	56.58	43.42	36.6	34.3	30.3	42.7	37.7	55.6	53.3	113	79	30		4		132

Phylogenetic analysis of Sorbus ser. Folgnerianae (Rosaceae)

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