Full-length transcriptome sequencing and annotation analyses of Bambusa multiplex sheath

doi:10.3969/j.issn.1000-2006.202002025

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2020, Vol. 44 ›› Issue (6): 175-183.doi: 10.3969/j.issn.1000-2006.202002025

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Full-length transcriptome sequencing and annotation analyses of Bambusa multiplex sheath

JU Ye¹^,²(), JIANG Jianping³, YIN Zengfang¹^,², WEI Qiang¹^,^*()

1. Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2. College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
3. Wanzai Forestry Bureau, Wanzai 336100, China

Received:2020-02-15 Revised:2020-03-22 Online:2020-11-30 Published:2020-12-07
Contact: WEI Qiang E-mail:296817241@qq.com;weiqiang@njfu.edu.cn

Abstract

Abstract:

【Objective】Currently, few reports have described the biological function of the bamboo sheath. This work aimed to elucidate the possible functions and the underlying biological mechanisms of the bamboo sheath from the perspective of molecular biology.【Method】Using PacBio Sequel full-length sequencing technology, we analyzed the transcriptomic profile of the culm sheath at different senescence stages of Bambusa multiplex.【Result】A total of 106 148 transcripts with an average length of 3 615 base pairs (bp) were obtained. Of those transcripts, 97.34% had annotated results. Mercator annotation further revealed that the transcripts covered all 34 functional subgroups associated with the bamboo sheath. The protein subgroup contained the most transcripts, with 18 224 transcripts. While the microRNA subgroup contained the least transcripts, with only nine being present in this subgroup. Additionally, 2 489 hormone-related transcripts and 8 804 transcription factors were detected. Interestingly, 393 transcripts related to photosynthesis were discovered in the full-length transcriptome of the B. multiplex sheath. A total of 189 transcripts encoding 30 NAC transcription factor genes were also identified. The expression of 93.33% of NAC transcription factor genes was found to be positively or negatively correlated with sheath senescence. Of them, seven NACs, including NAC002, NAC016, NAC017, NAC029(NAP), NAC042, NAC055 and NAC083 have been reported to play important roles in regulating leaf senescence; 14 NACs, including NAC014, have been reported to have potential roles in leaf senescence; and seven bamboo sheath senescence-associated NACs, including NAC025, NAC028, NAC045, NAC061, NAC086, NAC103 and NAC1L were newly discovered. The MISA software analysis revealed that 76 499 transcripts contain simple sequence repeats (SSRs). Most are single nucleotide repeat SSRs, accounting for 55.2% of all discovered SSRs. Additionally, 2 769 long non-coding RNAs (lncRNAs) were detected by using software such as PLRK et al.【Conclusion】These results revealed that various genes are actively expressed in the bamboo sheath. A number of transcripts related to all aspects of photosynthesis were detected in the bamboo sheath, indicating that the bamboo sheath may have the photosynthetic capacity. The majority of the identified NACs was associated with leaf senescence, suggesting a potential role of NACs in bamboo sheath senescence. Taken together, our work provides the first insights into the transcriptomic features of the bamboo sheath and provides a foundation for future studies to reveal the biological function of the bamboo sheath and the underlying molecular mechanisms of bamboo sheath senescence.

Key words: Bambusa multiplex, PacBio, simple sequence repeats(SSR), lncRNA, NAC, senescence

CLC Number:

S795
Q781

JU Ye, JIANG Jianping, YIN Zengfang, WEI Qiang. Full-length transcriptome sequencing and annotation analyses of Bambusa multiplex sheath[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2020, 44(6): 175-183.

Figures/Tables 7

Fig.1

Fig.2

Table 1

Transcripts involved in the photosynthesis of bamboo sheath"

光合作用过程 photosynthesis part	MapMan类别 MapMan Bin	转录本数目 transcript number	光合作用过程 photosynthesis part	MapMan类别 MapMan Bin	转录本数目 transcript number
卡尔文循环 calvin cycle	醛缩酶aldolase	11	光反应 light reaction	转酮醇酶transketolase	3
卡尔文循环 calvin cycle	醛缩酶aldolase	11		ATP合成酶ATPsynthase	12
	D-果糖1,6-二磷酸酯酶 D-fructose-1,6-bisphosphate 1-phosphohydrolase	2		ATP合成酶ATPsynthase	12
				循环电子流-叶绿体呼吸 cyclic electron flow-chlororespiration	26
				细胞色素b6/f cytochrome b6/f	4
	甘油醛-3-磷酸脱氢酶 glyceraldehyde-3-phosphate dehydrogenase	1		细胞色素b6/f cytochrome b6/f	4
				NADH脱氢酶NADH DH	12
				铁氧化还原蛋白ferredoxin	25
				质体醌plastocyanin	1
				光系统Ⅰ. LHC-Ⅰ photosystemI. LHC-Ⅰ	12
	磷酸甘油酸激酶 phosphoglycerate kinase	10		光系统Ⅰ. LHC-Ⅰ photosystemI. LHC-Ⅰ	12
	磷酸甘油酸激酶 phosphoglycerate kinase	10		光系统Ⅰ多肽亚基 photosystem Ⅰ. PSI polypeptide subunits	28
	磷酸戊糖激酶 phosphopentokinase	4		光系统Ⅰ多肽亚基 photosystem Ⅰ. PSI polypeptide subunits	28
	磷酸戊糖激酶 phosphopentokinase	4		光系统Ⅱ.生物发生 photosystem Ⅱ. Biogenesis	1
	核糖-5-磷酸异构酶 ribose 5-phosphate isomerase	1		光系统Ⅱ.生物发生 photosystem Ⅱ. Biogenesis	1
	核糖-5-磷酸异构酶 ribose 5-phosphate isomerase	1		光系统Ⅱ. LHC-Ⅱ photosystem Ⅱ. LHC-Ⅱ	20
	核酮糖磷酸3-表异构酶 ribulose-phosphate 3-epimerase	7		光系统Ⅱ. LHC-Ⅱ photosystem Ⅱ. LHC-Ⅱ	20
				光系统Ⅱ多肽亚基 photosystem Ⅱ. PSII polypeptide subunits	42
				状态转换state transition	24
	rubisco互作相关 rubisco interacting	30		状态转换state transition	24
	rubisco互作相关 rubisco interacting	30	光呼吸 photorespiration	过氧化物酶体转氨酶 aminotransferases peroxisomal	7
	rubisco大亚基 rubisco large subunit	6	光呼吸 photorespiration	过氧化物酶体转氨酶 aminotransferases peroxisomal	7
				甘油酸激酶glycerate kinase	9
				甘油酸清除. H蛋白 glycine cleavage. H protein	12
	rubisco小亚基 rubisco small subunit	4		甘油酸清除. H蛋白 glycine cleavage. H protein	12
				乙醇酸氧化酶glycolateoxidase	31
				羟基丙酮酸还原酶 hydroxy pyruvate reductase	17
	景天庚酮糖二磷酸酶 sedoheptulose bisphosphatase	2		羟基丙酮酸还原酶 hydroxy pyruvate reductase	17
	景天庚酮糖二磷酸酶 sedoheptulose bisphosphatase	2		磷酸甘油磷酸酯酶 phosphoglycolate phosphatase	5
	磷酸丙糖异构酶 triosephosphate isomerase	11		磷酸甘油磷酸酯酶 phosphoglycolate phosphatase	5
	磷酸丙糖异构酶 triosephosphate isomerase	11		丝氨酸羟甲基转移酶 serinehydroxy methyltransferase	1

Table 1

Fig.3

Fig.4

Table 2

Fig.5

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重复次数 replicates	重复基元长度及其数目 length of repeat motif and number
重复次数 replicates	单核苷酸 mononucleotide	二核苷酸 dinucleotide	三核苷酸 trinucleotide	四核苷酸 tetranucleotide	五核苷酸 pentanucleotide	六核苷酸 hexanucleotide
≥ 5~8	0	9 735	16 985	918	337	130
≥9~12	27 294	3 025	6 56	50	6	2
≥13~16	8 658	1 034	132	12	0	0
≥17~20	3 826	716	30	35	0	2
≥21~24	2 450	433	23	10	0	0
总数 total number	42 228	14 943	17 826	1 025	343	134
占比/% percentage	55.20	19.53	23.30	1.34	0.45	0.18

Full-length transcriptome sequencing and annotation analyses of Bambusa multiplex sheath

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