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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (6): 1020-1030.doi: 10.3724/SP.J.1006.2021.04042


Characterization of the expression profiling of circRNAs in the barks of stems in ramie

LI Fu(), WANG Yan-Zhou, YAN Li, ZHU Si-Yuan, LIU Tou-Ming*()   

  1. Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture and Rural Affairs/Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, Hunan, China
  • Received:2020-02-24 Accepted:2020-07-02 Online:2021-06-12 Published:2020-07-16
  • Contact: LIU Tou-Ming E-mail:704510340@qq.com;liutouming@caas.cn
  • Supported by:
    The National Natural Science Foundation of China(31871678);The Agricultural Science and Technology Innovation Program of China(CAAS-ASTIP-IBFC)


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

Fig. 1

A picture shows the sampling position for circRNA sequencing MPS and TPS represent the barks sample collected from the middle and top stems, respectively. This picture displays that the secondary cellular walls (SCWs) of fiber cells from the top of the ramie stems do not initiate growth and those from middle part of the ramie stems are thickening. This figure is cited from the study of Chen et al.[10] "

Table 1

Primer sequence of differentially expressed circRNAs and the control gene for qRT-PCR in ramie"

circRNA ID
Forward primer (5°-3°)
Reverse primer (5°-3°)

Table 2

Data statistics from circRNA sequencing for six samples of stem barks in ramie"

Raw read number (Million)
Clean read数
Clean read number (Million)
Total length
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

Fig. 2

GO functional classification of 4729 transcribed circRNAs genes in ramie"

Fig. 3

Identification of differentially expressed circRNA by comparing gene expression level between TPS and MPS libraries Red dots represent transcripts more prevalent in the MPS library, blue dots show those present at a lower frequency in the MPS, and gray dots indicate transcripts that did not change significantly; X and Y axes represent the logarithm of read number for each circRNA in TPS and MPS libraries, respectively. Abbreviations are the same as those given in Table 2."

Table 3

Detail for differentially expressed circRNA identified between the bast barks of MPS and TPS"

circRNA ID
MPS read数
MPS-reads number
TPS read数
TPS-reads number
Differential fold (MPS/TPS)
Direction regulated
Adjusted P-value
Gene located by circRNA
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

Fig. 4

Relative expression level of ten circRNAs stem bark tissues of MPS and TPS by qRT-PCR in ramie Abbreviations are the same as those given in Table 2."

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