Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan

doi:10.13560/j.cnki.biotech.bull.1985.2022-1369

Abstract

Abstract:

In order to analyze the structure and composition of the chloroplast genome of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, its evolutionary position in Colocasia genus and its difference from the chloroplast genome of the same genus were determined, which may provide relevant basis for species identification, genetic diversity analysis and resource protection of Colocasia genus. The Illumina NovaSeq 6000 sequencing platform was used to sequence the genome of the chloroplast of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan. Bioinformatics analysis methods were to conduct sequence assembly, annotation and feature analysis, and bioinformatics software such as Geneious, MISA, MAFF, FASTREE, CUSP, Chips and Codon W were used to analyze the genome structure and number, codon preference, sequence duplication, SSR sites and phylogeny. The results showed that the chloroplast genome size of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan was 162 544 bp, showing a tetrad structure. It contained 130 genes, including 84 protein coding genes, 37 tRNA genes, 8 ribosomal rRNA genes and 1 pseudogene. By codon preference analysis, the average number of effective codons was 45.60, and 39 genes with ENC value < 45, indicating strong codon preference. Through SSR analysis, 101 SSR sites were detected, of which single nucleotide repeats were the most（about 83.17%）, and single nucleotide was mainly A/T type. Compared with related species, the chloroplast genome sequence was highly conserved, especially the protein coding sequence was highly similar. In addition, the phylogenetic analysis showed that C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan was clustered into one branch with Colocasia genus and Remusatia genus. This study obtained the basic information of chloroplast genome and phylogenetic location of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, and provided a preliminary study for its species identification, genetic diversity of natural population and functional genomics.

Key words: Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, chloroplast genome characterization, phylogenetic analysis, SSR analysis, IR boundary analysis, codon preference

YIN Ming-hua, YU Huan-yuan, XIAO Xin-yi, WANG Yu-ting. Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan[J]. Biotechnology Bulletin, 2023, 39(6): 233-247.

Figures/Tables 15

References 34

[1]	刘星月, 朱强龙, 李慧英, 等. 红芽芋脱毒试管芋诱导及植株再生[J]. 园艺学报, 2020, 47(12): 2427-2438.
	Liu XY, Zhu QL, Li HY, et al. Induction and plant regeneration of virus-free microtuber in red bud taro[J]. Acta Hortic Sin, 2020, 47(12): 2427-2438. doi: 10.16420/j.issn.0513-353x.2020-0470
[2]	李云, 牛丽亚, 涂瑾, 等. 亲水胶体对红芽芋全粉理化特性和消化特性的影响[J]. 中国粮油学报, 2020, 35(2): 12-17.
	Li Y, Niu LY, Tu J, et al. Effect of hydrocolloids on physicochemical properties and digestive properties of red bud taro flour[J]. J Chin Cereals Oils Assoc, 2020, 35(2): 12-17.
[3]	邓接楼, 曹昊玮, 李玲, 等. 脱毒红芽芋试管芋盆栽种植的农艺性状分析[J]. 分子植物育种, 2019, 17(22): 7500-7506.
	Deng JL, Cao HW, Li L, et al. Analysis on agronomic traits of virus-free test-tube taro planted in pots[J]. Mol Plant Breed, 2019, 17(22): 7500-7506.
[4]	肖慈生, 方加军, 肖月土, 等. 铅山红芽芋早熟栽培技术规程[J]. 长江蔬菜, 2018(15): 29-30.
	Xiao CS, Fang JJ, Xiao YT, et al. Technical regulations for early maturing cultivation of Yanshan red bud taro[J]. J Chang Veg, 2018(15): 29-30.
[5]	余志平, 林海红, 余俊红, 等. 铅山红芽芋产业发展概况[J]. 长江蔬菜, 2016(20): 34-36.
	Yu ZP, Lin HH, Yu JH, et al. Development of red bud taro industry in Yanshan[J]. J Chang Veg, 2016(20): 34-36.
[6]	姜绍通, 程元珍, 郑志, 等. 红芽芋营养成分分析及评价[J]. 食品科学, 2012, 33(11): 269-272. doi: 10.7506/spkx1002-6630-201211057
	Jiang ST, Cheng YZ, Zheng Z, et al. Analysis and evaluation of nutritional components of red bud taro(Colocasia esulenla L. schott)[J]. Food Sci, 2012, 33(11): 269-272.
[7]	Wang QR, Huang ZR, Gao CS, et al. The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species[J]. Genetica, 2021, 149(5/6): 299-311. doi: 10.1007/s10709-021-00131-9
[8]	Zhao ZY, Wang X, Yu Y, et al. Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses[J]. PeerJ, 2018, 6: e6032. doi: 10.7717/peerj.6032 URL
[9]	Daniell H, Lin CS, Yu M, et al. Chloroplast genomes: diversity, evolution, and applications in genetic engineering[J]. Genome Biol, 2016, 17(1): 134. doi: 10.1186/s13059-016-1004-2 pmid: 27339192
[10]	Ahmed I, Matthews PJ, Biggs PJ, et al. Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta(L.)Schott(Araceae)and closely related taxa[J]. Mol Ecol Resour, 2013, 13(5): 929-937. doi: 10.1111/men.2013.13.issue-5 URL
[11]	Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data[J]. Nucleic Acids Res, 2017, 45(4): e18.
[12]	Tillich M, Lehwark P, Pellizzer T, et al. GeSeq - versatile and accurate annotation of organelle genomes[J]. Nucleic Acids Res, 2017, 45(W1): W6-W11. doi: 10.1093/nar/gkx391 URL
[13]	Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Res, 1997, 25(5): 955-964. doi: 10.1093/nar/25.5.955 pmid: 9023104
[14]	Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW(OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes[J]. Curr Genet, 2007, 52(5/6): 267-274. doi: 10.1007/s00294-007-0161-y URL
[15]	Thiel T, Michalek W, Varshney RK, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley(Hordeum vulgare L.)[J]. Theor Appl Genet, 2003, 106(3): 411-422. doi: 10.1007/s00122-002-1031-0 pmid: 12589540
[16]	Low SL, Yu CC, Ooi IH, et al. Extensive Miocene speciation in and out of Indochina: the biogeographic history of Typhonium sensu stricto(Araceae)and its implication for the assembly of Indochina flora[J]. J Syst Evol, 2021, 59(3): 419-428. doi: 10.1111/jse.v59.3 URL
[17]	Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Mol Biol Evol, 2013, 30(4): 772-780. doi: 10.1093/molbev/mst010 pmid: 23329690
[18]	Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments[J]. PLoS One, 2010, 5(3): e9490. doi: 10.1371/journal.pone.0009490 URL
[19]	Sun LY, Jiang Z, Wan XX, et al. The complete chloroplast genome of Magnolia polytepala: comparative analyses offer implication for genetics and phylogeny of Yulania[J]. Gene, 2020, 736: 144410. doi: 10.1016/j.gene.2020.144410 URL
[20]	Ahmed I, Biggs PJ, Matthews PJ, et al. Mutational dynamics of aroid chloroplast genomes[J]. Genome Biol Evol, 2012, 4(12): 1316-1323. doi: 10.1093/gbe/evs110 pmid: 23204304
[21]	Gao LQ, Li YL, Guo CC, et al. Indocalamus chongzhouensis(Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data[J]. Phytotaxa, 2022, 542(1): 53-63. doi: 10.11646/phytotaxa.542.1 URL
[22]	Romero H, Zavala A, Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces[J]. Nucleic Acids Res, 2000, 28(10): 2084-2090. doi: 10.1093/nar/28.10.2084 pmid: 10773076
[23]	Carlini DB, Chen Y, Stephan W. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr[J]. Genetics, 2001, 159(2): 623-633. doi: 10.1093/genetics/159.2.623 pmid: 11606539
[24]	Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis[J]. Proc Natl Acad Sci USA, 1999, 96(8): 4482-4487. doi: 10.1073/pnas.96.8.4482 pmid: 10200288
[25]	Sharp PM, Emery LR, Zeng K. Forces that influence the evolution of codon bias[J]. Philos Trans R Soc Lond B Biol Sci, 2010, 365(1544): 1203-1212. doi: 10.1098/rstb.2009.0305 URL
[26]	Takahashi D, Sakaguchi S, Isagi Y, et al. Comparative chloroplast genomics of series Sakawanum in genus Asarum(Aristolochiaceae)to develop single nucleotide polymorphisms(SNPs)and simple sequence repeat(SSR)markers[J]. J For Res, 2018, 23(6): 387-392. doi: 10.1080/13416979.2018.1518649 URL
[27]	Yamane K, Kawahara T. Size homoplasy and mutational behavior of chloroplast simple sequence repeats(cpSSRs)inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid Triticum and Aegilops species[J]. Genet Resour Crop Evol, 2018, 65(3): 727-743. doi: 10.1007/s10722-017-0567-4 URL
[28]	Dugas DV, Hernandez D, Koenen EJM, et al. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP[J]. Sci Rep, 2015, 5: 16958. doi: 10.1038/srep16958 pmid: 26592928
[29]	Park S, An B, Park S. Reconfiguration of the plastid genome in Lamprocapnos spectabilis: IR boundary shifting, inversion, and intraspecific variation[J]. Sci Rep, 2018, 8(1): 13568. doi: 10.1038/s41598-018-31938-w
[30]	Raubeson LA, Peery R, Chumley TW, et al. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus[J]. BMC Genomics, 2007, 8: 174. pmid: 17573971
[31]	Li X, Li Y, Zang M, et al. Complete chloroplast genome sequence and phylogenetic analysis of Quercus acutissima[J]. Int J Mol Sci, 2018, 19(8): E2443.
[32]	Gu C, Ma L, Wu Z, et al. Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales[J]. BMC Plant Biol, 2019, 19(1): 281. doi: 10.1186/s12870-019-1870-3 pmid: 31242865
[33]	Dong WP, Xu C, Li CH, et al. ycf1, the most promising plastid DNA barcode of land plants[J]. Sci Rep, 2015, 5: 8348. doi: 10.1038/srep08348 pmid: 25672218
[34]	Amar MH. ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica[J]. J Genet Eng Biotechnol, 2020, 18(1): 42. doi: 10.1186/s43141-020-00057-3

基因分类 Category	基因分组 Gene group	基因名称 Gene name
光合作用 Photosynthesis	光合系统I基因 Photosystem I	psaA、psaB、psaC、psaI、psaJ
	光合系统II基因 Photosystem II	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbK、psbL、psbM、psbT、psbZ
	细胞色素复合物基因 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN
	ATP合成酶基因 ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI
	NADH脱氢酶基因 NADH dehydrogenase	ndhA、ndhB（2）、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK
	二磷酸核酮糖羧化酶大亚基基因 Rubisco large subunit	rbcL
自我复制Self-replication	RNA聚合酶亚基基因RNA polymeras	rpoA、rpoB、rpoC1、rpoC2
	核糖体小亚基基因 Ribosomal proteins（SSU）	rps11、rps12（2）、rps14、rps15、rps16、rps18、 rps19、rps2、rps3、rps4、rps7（2）、rps8
	核糖体大亚基基因 Ribosomal proteins（LSU）	rpl14、rpl16、rpl2（2）、rpl20、rpl22、rpl23（2）、rpl32、rpl33、rpl36、
	转运RNA基因 Transfer RNAs	trnC-GCA、trnD-GUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU（2）、trnK-UUU、trnL-CAA（2）、trnL-UAA、trnL-UAG、trnM-CAU、trnN-GUU（2）、trnP-UGG、trnQ-UUG、trnR-ACG（2）、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-UGU、trnV-GAC（2）、trnV-UAC、trnW-CCA、trnY-GUA、trnfM-CAU
	核糖体RNA基因 Ribosomal RNAs	rrn16（2）、rrn23（2）、rrn4.5（2）、rrn5（2）
其他基因 Other genes	成熟酶基因 Maturase	matK
	蛋白酶Protease	clpP1
	乙酰辅酶 A 羧化酶Acetyl-CoA carboxylase	accD
	翻译起始因子 Translation initiation factor	infA
	包膜蛋白基因 Envelope membrane protein	cemA
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
未知功能Unknown function	假定叶绿体阅读框 Hypothetical chloroplast reading frames	ycf1、ycf2（2）

基因分类 Category	基因分组 Gene group	基因名称 Gene name
光合作用 Photosynthesis	光合系统I基因 Photosystem I	psaA、psaB、psaC、psaI、psaJ
	光合系统II基因 Photosystem II	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbK、psbL、psbM、psbT、psbZ
	细胞色素复合物基因 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN
	ATP合成酶基因 ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI
	NADH脱氢酶基因 NADH dehydrogenase	ndhA、ndhB（2）、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK
	二磷酸核酮糖羧化酶大亚基基因 Rubisco large subunit	rbcL
自我复制Self-replication	RNA聚合酶亚基基因RNA polymeras	rpoA、rpoB、rpoC1、rpoC2
	核糖体小亚基基因 Ribosomal proteins（SSU）	rps11、rps12（2）、rps14、rps15、rps16、rps18、 rps19、rps2、rps3、rps4、rps7（2）、rps8
	核糖体大亚基基因 Ribosomal proteins（LSU）	rpl14、rpl16、rpl2（2）、rpl20、rpl22、rpl23（2）、rpl32、rpl33、rpl36、
	转运RNA基因 Transfer RNAs	trnC-GCA、trnD-GUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU（2）、trnK-UUU、trnL-CAA（2）、trnL-UAA、trnL-UAG、trnM-CAU、trnN-GUU（2）、trnP-UGG、trnQ-UUG、trnR-ACG（2）、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-UGU、trnV-GAC（2）、trnV-UAC、trnW-CCA、trnY-GUA、trnfM-CAU
	核糖体RNA基因 Ribosomal RNAs	rrn16（2）、rrn23（2）、rrn4.5（2）、rrn5（2）
其他基因 Other genes	成熟酶基因 Maturase	matK
	蛋白酶Protease	clpP1
	乙酰辅酶 A 羧化酶Acetyl-CoA carboxylase	accD
	翻译起始因子 Translation initiation factor	infA
	包膜蛋白基因 Envelope membrane protein	cemA
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
未知功能Unknown function	假定叶绿体阅读框 Hypothetical chloroplast reading frames	ycf1、ycf2（2）

区域Area	碱基长度 Base length/ bp	T/%	C/%	A/%	G/%	GC/%	AT偏斜值AT skew	GC 偏斜值GC skew
大单拷贝区LSC	89 814	33.58	17.59	32.04	16.79	34.38	-0.023 5	-0.023 3
小单拷贝区SSC	22 074	36.02	15.12	34.97	13.89	29.01	-0.014 8	-0.042 4
反向重复序列a（IRa）	25 328	29.01	21.95	28.59	20.44	42.40	-0.007 3	-0.035 6
反向重复序列b（IRb）	25 328	28.59	20.44	29.01	21.95	42.40	0.007 3	0.035 6
总基因组	162 544	32.42	18.38	31.43	17.77	36.15	-0.015 5	-0.016 9

区域Area	碱基长度 Base length/ bp	T/%	C/%	A/%	G/%	GC/%	AT偏斜值AT skew	GC 偏斜值GC skew
大单拷贝区LSC	89 814	33.58	17.59	32.04	16.79	34.38	-0.023 5	-0.023 3
小单拷贝区SSC	22 074	36.02	15.12	34.97	13.89	29.01	-0.014 8	-0.042 4
反向重复序列a（IRa）	25 328	29.01	21.95	28.59	20.44	42.40	-0.007 3	-0.035 6
反向重复序列b（IRb）	25 328	28.59	20.44	29.01	21.95	42.40	0.007 3	0.035 6
总基因组	162 544	32.42	18.38	31.43	17.77	36.15	-0.015 5	-0.016 9

核苷酸类型 Nucleotide type	简单重复序列 Simple sequence repeat	重复序列个数 Number of SSR
单核苷酸 Mononucleotide	A	45
	C	2
	G	1
	T	36
二核苷酸 Dinucleotide	AT	5
二核苷酸 Dinucleotide	TA	10
三核苷酸 Trinucleotide	TTA	1
四核苷酸 Tetranucleotide	TATG	1