苎麻茎皮环状RNA表达谱分析

doi:10.3724/SP.J.1006.2021.04042

摘要/Abstract

摘要：

苎麻[Boehmeria nivea (L.) Gaud.]是我国特色的天然纤维作物, 其纤维具有拉伸力强、纤维束长等特点。解析苎麻纤维发育调控机制, 对实现纤维产量和品质性状遗传改良具有重要意义。本研究基于高通量测序技术开展了苎麻茎顶部和中部的茎皮组织环状RNA (circRNA)分析, 在2个组织中共鉴定到5268个苎麻circRNA。比较circRNA的表达水平发现, 78个circRNA在2个组织中呈现差异表达。因苎麻茎中部韧皮纤维处于生长发育期, 而茎顶部韧皮纤维尚未起始生长, 推测这78个circRNA是纤维不同发育时期差异表达基因, 它们可能参与了苎麻的纤维发育调控。研究结果将为解析circRNA调控苎麻纤维生长发育机制奠定基础。

关键词: 苎麻, 纤维发育, 环状RNA, 差异表达

Abstract:

Ramie [Boehmeria nivea (L.) Gaud.] is a special natural fiber crops in China, and its fiber has many excellent characteristics, including long strands and well tensile strength. Elucidation of the mechanism for fiber formation will be helpful for the improvement of fiber yield and quality in ramie. In this study, the expressed analysis of circular RNA (circRNA) for the tissues of barks from the top stems and middle stems were performed by Illumina sequencing, respectively. The total of 5268 circRNAs were identified. Among these circRNAs, 78 showed differential expression between two examined tissues. Previous cytological observation suggested that the secondary cellular walls (SCWs) of fiber cells from the top of the ramie stems did not initiate growth and those from middle part of the ramie stems were thickening. Therefore, we speculated that these 78 differentially expressed circRNAs were potentially involved in the fiber development in ramie. The results provide an important basis for understanding the role of circRNA in the regulation of fiber development.

Key words: ramie, fiber development, circRNA, differential expression

李富, 王延周, 严理, 朱四元, 刘头明. 苎麻茎皮环状RNA表达谱分析[J]. 作物学报, 2021, 47(6): 1020-1030.

LI Fu, WANG Yan-Zhou, YAN Li, ZHU Si-Yuan, LIU Tou-Ming. Characterization of the expression profiling of circRNAs in the barks of stems in ramie[J]. Acta Agronomica Sinica, 2021, 47(6): 1020-1030.

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链接本文: https://zwxb.chinacrops.org/CN/10.3724/SP.J.1006.2021.04042

https://zwxb.chinacrops.org/CN/Y2021/V47/I6/1020

图/表 7

图1

表1

表2

图2

图3

表3

苎麻MPS和TPS茎皮中差异表达circRNA信息表"

circRNA名称 circRNA ID	类型 Type	MPS read数 MPS-reads number	TPS read数 TPS-reads number	差异倍数 Differential fold (MPS/TPS)	调控方向 Direction regulated	校正P值 Adjusted P-value	对应基因 Gene located by circRNA	对应基因功能 Annotationof gene located by circRNA
scaffold13:3497301\|3498287	Introgenic	553.7	13.0	42.7	上调 Up-regulated	2.6E-04	whole_GLEAN_10021135	Ent-kaurenoic acid oxidase 1
scaffold7:2328081\|2328970	Iintrogenic	760.3	18.1	42.0	上调Up-regulated	2.8E-04	whole_GLEAN_10025341	Casein kinase 1
scaffold27:618745\|619712	Introgenic	484.5	12.5	38.9	上调Up-regulated	3.9E-04	whole_GLEAN_10015712	Cleavage and polyadenylation specificity factor subunit 3-I
scaffold24:109942\|110887	Introgenic	461.0	12.8	35.9	上调Up-regulated	5.4E-04	whole_GLEAN_10016716	Protein APEM9
scaffold68:19731\|20827	Introgenic	433.3	12.1	35.7	上调Up-regulated	5.6E-04	whole_GLEAN_10010106	Protein CHROMATIN REMODELING 5
scaffold777:22008\|22923	Introgenic	485.5	14.2	34.2	上调Up-regulated	6.7E-04	whole_GLEAN_10001638	Non-specific phospholipase C3
scaffold1:1651705\|1652476	Introgenic	507.7	14.9	34.1	上调Up-regulated	6.7E-04	whole_GLEAN_10029483	Monogalactosyldiacylglycerol synthase
scaffold11:2168138\|2169190	Intergenic	401.2	11.8	33.9	上调Up-regulated	6.8E-04
scaffold14:2019005\|2020131	Introgenic	568.2	17.5	32.4	上调Up-regulated	8.2E-04	whole_GLEAN_10020529	Peroxisome biogenesis protein 1
scaffold1:2974233\|2974487	Introgenic	418.1	13.7	30.6	上调Up-regulated	1.0E-03	whole_GLEAN_10029667	Homeobox protein knotted-1-like 1
scaffold4:2794969\|2795547	Introgenic	328.8	10.8	30.5	上调Up-regulated	1.0E-03	whole_GLEAN_10027195	Lissencephaly-1 homolog
scaffold13:1482426\|1482614	Introgenic	288.1	10.8	26.7	上调Up-regulated	1.7E-03	whole_GLEAN_10020870	Threonine-protein kinase PBL28
scaffold42:394825\|395928	Introgenic	303.4	11.9	25.5	上调Up-regulated	2.0E-03	whole_GLEAN_10012793	U11/U12 small nuclear ribonucleoprotein 65 kDa protein
scaffold110:48151\|61235	Introgenic	256.8	10.3	24.9	上调Up-regulated	2.2E-03	whole_GLEAN_10007543	Protein TIC 40
scaffold6:1851520\|1851960	Introgenic	400.8	16.3	24.5	上调Up-regulated	2.3E-03	whole_GLEAN_10025870	DEAD-box ATP-dependent RNA helicase 50
scaffold6:319819\|320593	Introgenic	239.6	10.5	22.9	上调Up-regulated	2.9E-03	whole_GLEAN_10025672	GBF-interacting protein 1
scaffold22:2080855\|2081636	Introgenic	308.2	13.6	22.6	上调Up-regulated	3.1E-03	whole_GLEAN_10017734	SOK1 kinase belonging to the STE20/SPS1/GC kinase family
scaffold38:1007107\|1007440	Introgenic	229.5	10.2	22.5	上调Up-regulated	3.1E-03	whole_GLEAN_10013247	Lipoxygenase 6
scaffold4:984097\|984791	Introgenic	225.4	10.3	21.8	上调Up-regulated	3.5E-03	whole_GLEAN_10026982	V-type proton ATPase subunit a1
scaffold36:1130226\|1130557	Introgenic	332.4	15.3	21.8	上调Up-regulated	3.5E-03	whole_GLEAN_10013939	Primary amine oxidase
scaffold9:3087645\|3088126	Introgenic	261.8	12.2	21.5	上调Up-regulated	3.7E-03	whole_GLEAN_10024168	Transcription factor bHLH144
scaffold69:390306\|390963	Introgenic	230.6	11.2	20.6	上调Up-regulated	4.2E-03	whole_GLEAN_10010042	Formin-like protein 16
scaffold244:78865\|79334	Introgenic	216.4	10.9	19.9	上调Up-regulated	4.7E-03	whole_GLEAN_10004368	Uncharacterized mitochondrial protein ymf40
scaffold11:2226699\|2233286	Introgenic	273.2	13.9	19.6	上调Up-regulated	4.9E-03	whole_GLEAN_10021948	Cold-regulated 413 plasma membrane protein 2
scaffold23:488065\|489466	Introgenic	198.8	10.2	19.4	上调Up-regulated	5.1E-03	whole_GLEAN_10017916	Phosphoinositide phosphatase SAC1
scaffold59:336176\|337027	Introgenic	192.9	10.1	19.1	上调Up-regulated	5.4E-03	whole_GLEAN_10011259	Glycosylphosphatidylinositol anchor synthesis protein
scaffold270:63772\|64261	Introgenic	215.3	11.3	19.0	上调Up-regulated	5.5E-03	whole_GLEAN_10004135	ATP synthase protein YMF19
scaffold21:626345\|627257	Introgenic	179.7	9.7	18.6	上调Up-regulated	5.9E-03	whole_GLEAN_10019902	Poly [ADP-ribose] polymerase 1
scaffold41:981509\|982441	Introgenic	232.5	12.9	18.0	上调Up-regulated	6.5E-03	whole_GLEAN_10013030	WD40 repeat protein
scaffold25:1518597\|1519148	Introgenic	183.3	10.3	17.7	上调Up-regulated	6.8E-03	whole_GLEAN_10016591	Protein LSD1
scaffold69:199217\|199851	Introgenic	194.3	11.2	17.3	上调Up-regulated	7.4E-03	whole_GLEAN_10010022	U-box domain-containing protein 14
scaffold37:1378235\|1379257	Introgenic	163.1	9.5	17.2	上调Up-regulated	7.5E-03	whole_GLEAN_10013509	Uncharacterized protein At1g51745
scaffold41:312471\|314479	Introgenic	168.0	10.2	16.5	上调Up-regulated	8.5E-03	whole_GLEAN_10012948	Nucleolar GTPase 2
scaffold30:600099\|602644	Introgenic	156.9	9.6	16.3	上调Up-regulated	8.9E-03	whole_GLEAN_10015039	Protein CROWDED NUCLEI 3
scaffold34:2347785\|2349055	Introgenic	144.0	9.0	16.0	上调Up-regulated	9.3E-03	whole_GLEAN_10017394	B3 domain-containing protein07g0563300
scaffold360:24869\|25462	Introgenic	174.8	11.0	15.9	上调Up-regulated	9.4E-03	whole_GLEAN_10003361	Cytochrome c oxidase subunit 2
scaffold1:5693805\|5694897	Introgenic	169.3	10.6	15.9	上调Up-regulated	9.5E-03	whole_GLEAN_10030060	Internal alternative NAD(P)H-ubiquinone oxidoreductase A1
scaffold244:79500\|79823	Introgenic	155.0	9.9	15.7	上调Up-regulated	9.8E-03	whole_GLEAN_10004368	Uncharacterized mitochondrial protein ymf40
scaffold270:63801\|64263	Introgenic	155.3	10.1	15.4	上调Up-regulated	1.0E-02	whole_GLEAN_10004135	ATP synthase protein YMF19
scaffold112:248381\|248869	Introgenic	148.3	9.6	15.4	上调Up-regulated	1.0E-02	whole_GLEAN_10007469	Peptidyl-prolyl cis-trans isomerase CYP71
scaffold36:1536277\|1547559	Introgenic	150.7	9.9	15.2	上调Up-regulated	1.1E-02	whole_GLEAN_10013997	Cytochrome P450 71A1
scaffold360:12593\|13058	Intergenic	155.4	10.4	15.0	上调Up-regulated	1.1E-02
scaffold1:142468\|143089	Introgenic	128.5	9.0	14.3	上调Up-regulated	1.3E-02	whole_GLEAN_10029278	Protein Mut11
scaffold29:718451\|719832	Introgenic	122.4	8.8	13.9	上调Up-regulated	1.4E-02	whole_GLEAN_10015276	E4 SUMO-protein ligase PIAL2
scaffold360:15097\|17687	Introgenic	121.8	8.8	13.9	上调Up-regulated	1.4E-02	whole_GLEAN_10003361	Cytochrome c oxidase subunit 2
scaffold39:1205365\|1205747	Intergenic	121.1	8.9	13.6	上调Up-regulated	1.5E-02
scaffold19:1034720\|1049699	Introgenic	115.4	8.8	13.1	上调Up-regulated	1.6E-02	whole_GLEAN_10018479	Short-chain dehydrogenase/reductase 2b
scaffold27:1733501\|1744156	Introgenic	102.4	8.0	12.8	上调Up-regulated	1.7E-02	whole_GLEAN_10015833	Large ribosomal RNA subunit accumulation protein YCED homolog 2
scaffold270:115352\|115747	Introgenic	98.1	7.7	12.7	上调Up-regulated	1.8E-02	whole_GLEAN_10004138	Hypothetical protein
scaffold11:3427880\|3429252	Introgenic	95.6	7.8	12.3	上调Up-regulated	2.0E-02	whole_GLEAN_10022104	Probable ubiquitin-like-specific protease 2B
scaffold5:2904984\|2905988	Introgenic	96.1	7.9	12.1	上调Up-regulated	2.0E-02	whole_GLEAN_10026531	Transcription factor bHLH68
scaffold22:2902269\|2903224	Introgenic	1019.2	88.3	11.5	上调Up-regulated	2.0E-02	whole_GLEAN_10017861	TATA-binding protein-associated factor BTAF1
scaffold41:1051261\|1051835	Introgenic	333.0	30.0	11.1	上调Up-regulated	2.5E-02	whole_GLEAN_10013037	Probable E3 ubiquitin-protein ligase RHB1A
scaffold423:8362\|8891	Introgenic	75.7	6.9	11.0	上调Up-regulated	2.6E-02	whole_GLEAN_10002921	NADH-ubiquinone oxidoreductase chain 2
scaffold50:971580\|972301	Introgenic	75.7	6.9	11.0	上调Up-regulated	2.6E-02	whole_GLEAN_10022800	Uncharacterized conserved protein
scaffold29:144492\|145002	Introgenic	1922.2	200.1	9.6	上调Up-regulated	2.6E-02	whole_GLEAN_10015203	A Plastidial ribosomal protein S1
scaffold423:7458\|7843	Introgenic	69.4	6.5	10.6	上调Up-regulated	2.8E-02	whole_GLEAN_10002921	NADH-ubiquinone oxidoreductase chain 2
scaffold41:1051261\|1051640	Introgenic	383.7	36.9	10.4	上调Up-regulated	3.0E-02	whole_GLEAN_10013037	Probable E3 ubiquitin-protein ligase RHB1A
scaffold128:291760\|298584	Introgenic	244.6	25.7	9.5	上调Up-regulated	3.7E-02	whole_GLEAN_10007591	Histone-lysine N-methyltransferase ATXR6
scaffold42:575382\|577290	Introgenic	248.1	26.2	9.5	上调Up-regulated	3.7E-02	whole_GLEAN_10012809	Uncharacterized conserved protein
scaffold4:4247567\|4248126	Introgenic	238.8	25.3	9.4	上调Up-regulated	3.8E-02	whole_GLEAN_10027396	ALBINO3-like protein 2
scaffold26:228677\|229118	Introgenic	233.3	25.6	9.1	上调Up-regulated	4.1E-02	whole_GLEAN_10016157	Protein BTR1
scaffold81:336505\|338444	Introgenic	223.2	24.5	9.1	上调Up-regulated	4.1E-02	whole_GLEAN_10009183	Protein FORGETTER 1
scaffold8:474393\|475508	Introgenic	633.7	72.5	8.7	上调Up-regulated	4.1E-02	whole_GLEAN_10024439	Uncharacterized protein At3g06530
scaffold3:3339987\|3341286	Introgenic	246.4	27.5	8.9	上调Up-regulated	4.2E-02	whole_GLEAN_10028049	Aspartate aminotransferase 3
scaffold133:143853\|144812	Introgenic	212.1	23.8	8.9	上调Up-regulated	4.3E-02	whole_GLEAN_10006440	Protein RNA-directed DNA methylation 3
scaffold16:2445618\|2446250	Introgenic	203.6	23.3	8.7	上调Up-regulated	4.5E-02	whole_GLEAN_10019477	Alternative NAD(P)H-ubiquinone oxidoreductase C1
scaffold270:115352\|115722	Introgenic	202.7	23.3	8.7	上调Up-regulated	4.5E-02	whole_GLEAN_10004138	Hypothetical protein
scaffold8:2674752\|2676656	Introgenic	580.2	69.2	8.4	上调Up-regulated	4.6E-02	whole_GLEAN_10024738	COMPASS-like H3K4 histone methylase component WDR5A
scaffold360:11517\|11838	Intergenic	560.1	68.9	8.1	上调Up-regulated	4.9E-02
scaffold12:2523138\|2525034	Introgenic	529.5	65.4	8.1	上调Up-regulated	4.9E-02	whole_GLEAN_10021469	Tetraspanin-18
scaffold40:1450202\|1450949	Introgenic	188.2	22.5	8.3	上调Up-regulated	5.0E-02	whole_GLEAN_10013727	Proline-rich receptor-like protein kinase PERK8
scaffold270:40371\|40783	Introgenic	991.9	121.6	8.2	上调Up-regulated	5.0E-02	whole_GLEAN_10004133	Hypothetical protein
scaffold7:3133443\|3134407	Introgenic	218.9	26.3	8.3	上调Up-regulated	5.0E-02	whole_GLEAN_10025435	DEAD-box ATP-dependent RNA helicase 13
scaffold69:125839\|129078	Introgenic	195.2	23.4	8.3	上调Up-regulated	5.0E-02	whole_GLEAN_10010014	Exocyst complex component EXO70A1
scaffold38:37152\|37816	Introgenic	181.8	22.1	8.2	上调Up-regulated	5.0E-02	whole_GLEAN_10013105	DNA replication licensing factor MCM2
scaffold9:1148862\|1149242	Introgenic	196.3	24.4	8.0	上调Up-regulated	5.0E-02	whole_GLEAN_10023894	Pyrophosphate-energized vacuolar membrane proton pump
scaffold2:6347151\|6348009	Introgenic	9.1	105.2	11.5	下调Down-regulated	2.3E-02	whole_GLEAN_10029246	N-Acetylglucosamine kinase

表3

图4

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circRNA名称 circRNA ID	正向引物 Forward primer (5°-3°)	反向引物 Reverse primer (5°-3°)
scaffold270:40371\|40783	TGGCATGAATCACCGAACCTG	TGTCATGACGCGCCCATTCCT
scaffold6:1851520\|1851960	ATGAAATCAGGGAATGCCAA	CTCCCAAACTTCACCGTC
scaffold360:24869\|25462	CTTTCCTTGCTTCGCCAAC	TTCCCTGCTACTCTATTGCT
scaffold360:11517\|11838	TCCACTAGCGTCATTCGAAG	CTAGGTCAGAAAAGCGAGAAC
scaffold36:1536277\|1547559	TTGATCTTGGCCATGTCCCGA	ACGGTTCAATAAGGCGAGA
scaffold110:48151\|61235	AGAATCCACAATACCGTCAGC	TTGTGTATTCATTTGGCCCAT
scaffold30:600099\|602644	ATAAAGAGTCGTTGGGCCTT	TGAACTTCCTTTCCGCCAGA
scaffold11:2168138\|2169190	GTCCACAGAGCGATCATATGTC	TTTTAGGCACTTACCGGGTT
scaffold360:15097\|17687	CGTTTGACTTGATCCCGACAG	CAGAGCAAATGAGGGTATAGCAA
scaffold128:291760\|298584	ACAAAAAGCAATGGCAATTACGG	AACAGACTCACCAATGGCATC
18S	ATGATAACTCGACGGATCGC	CTTGGATGTGGTAGCCGTTT

样品 Sample	原始read数 Raw read number (Million)	Clean read数 Clean read number (Million)	总长度 Total length (Gb)	Q30值 Q30 value (%)	Clean reads产出率 Yielded ratio of clean reads (%)
MPS1	101.23	74.3	11.1	96.4	73.4
MPS2	106.02	74.5	11.2	96.0	70.3
MPS3	107.77	74.3	11.1	96.7	68.9
TPS1	102.76	74.0	11.1	96.0	72.0
TPS2	119.18	73.7	11.1	96.1	61.9
TPS3	109.41	73.7	11.1	96.4	67.4