[1]邵欣瑜,熊星,杨峰,等.月月竹竹秆变色后全长转录组分析[J].江苏农业学报,2024,(03):538-551.[doi:doi:10.3969/j.issn.1000-4440.2024.03.017]
　SHAO Xin-yu,XIONG Xing,YANG Feng,et al.Full-length transcriptome sequencing analysis of Chimonobambusa sichuanensis after discoloration of bamboo culm[J].,2024,(03):538-551.[doi:doi:10.3969/j.issn.1000-4440.2024.03.017]
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月月竹竹秆变色后全长转录组分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2024年03期
页码:
538-551
栏目:
园艺
出版日期:
2024-03-30

文章信息/Info

Title:
Full-length transcriptome sequencing analysis of Chimonobambusa sichuanensis after discoloration of bamboo culm
作者:
邵欣瑜1; 熊星1; 杨峰2; 赵云飞3; 刘昌来1; 刘国华1
(1.南京林业大学竹类研究所/南方现代林业协同创新中心,江苏南京210037；2.菏泽化工高级技工学校,山东菏泽274500；3.临沂市公安局,山东临沂276000)
Author(s):
SHAO Xin-yu1; XIONG Xing1; YANG Feng2; ZHAO Yun-fei3; LIU Chang-lai1; LIU Guo-hua1
(1.Bamboo Research Institute, Nanjing Forestry University/Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China；2.Heze College of Chemical Technology, Heze 274500, China；3.Linyi Municipal Public Security Bureau, Linyi 276000, China)
关键词:
月月竹; 变色竹秆; 全长转录组测序; 光信号
Keywords:
Chimonobambusa sichuanensis; color-changing bamboo culm; full-length transcriptome sequencing; light signal
分类号:
S795.6
DOI:
doi:10.3969/j.issn.1000-4440.2024.03.017
摘要:
为探究月月竹竹秆受到光照由绿色变为紫色的分子机制,本研究采集月月竹同一竹节紫色部分(Z)、渐变部分(M)和绿色部分(L)的竹青,提取RNA,利用PacBio Sequel三代全长转录组测序技术,结合生物信息学方法对不同颜色的竹青进行全长转录组分析。结果表明,经过三代测序和数据质量控制,共获得非冗余转录本66 961条,长度为500～3 000 bp,平均长度1 389.22 bp,序列总长度为93.02 Mbp,N50为1 830 bp,G+C碱基含量为49.56%。利用NR、Swiss-Prot、COG、GO、KEGG和Pfam数据库对所有转录本进行功能注释,共有56 938条转录本被成功注释,占全部转录本的85.03%；49 115条转录本被GO注释,其中催化活性、细胞器、代谢过程分别是GO数据库分子功能、细胞组分和生物过程中含转录本最多的项目；28 231个转录本被KEGG数据库注释,其中与碳水化合物代谢和基因翻译相关的转录本最多。结合GO注释和KEGG注释,66 961条转录本中有381条转录本与光信号的感受、传递以及光调控相关,包括红光和远红光的受体蛋白PHYA、PHYB及信号通路蛋白PIF3、ELF3,蓝光的受体蛋白CRY、ZTL及信号通路蛋白COP1、SPA1、ELF3、GI、HY5等。类黄酮(包括花青素)代谢、叶绿素合成、类胡萝卜素合成等与植物色素合成相关通路分别含有转录本187条、44条和72条。全长转录本共获得2 079个转录因子,其中包括18个由35个转录本编码的与花青素合成相关的R2R3MYB转录因子。CNCI、CPC、Pfam、PLEK等数据库同时注释到的长链非编码RNA(LncRNA)6 359个,数量高于孝顺竹等其他竹种。本研究获得了高质量的月月竹竹青全长转录组数据，与竹秆变色相关的红光和蓝光受体及光信号传递蛋白，与花青素、叶绿素和类胡萝卜素合成相关的转录因子及长链非编码RNA（LncRNA）,为进一步深入分析月月竹竹秆变色机制提供基础。
Abstract:
In order to explore the molecular mechanism of bamboo culm changing from green to purple under light, we collected the purple part (Z), median part (M) and green part (L) of the same bamboo node, extracted RNA, and used PacBio Sequel three-generation full-length transcriptome sequencing technology combined with bioinformatics methods to analyze the full-length transcriptome of bamboo barks with different colors. The results showed that a total of 66 961 non-redundant transcripts were obtained after three generations of sequencing and data quality control. The length ranged from 500 bp to 3 000 bp, with an average length of 1 389.22 bp. The total length of the sequence was 93.02 Mbp, the N50 was 1 830 bp, and the G+C base content was 49.56%. A total of 56 938 transcripts were successfully annotated based on NR, Swiss-Prot, COG, GO, KEGG, and Pfam databases, accounting for 85.03% of all transcripts. A total of 49 115 transcripts were annotated by GO database, among which catalytic activity, organelle and metabolic process were the items with the most transcripts in molecular function, cellular component and biological process of GO database, respectively. The 28 231 transcripts were annotated by KEGG database, of which the transcripts related to carbohydrate metabolism and gene translation were the most. Combined with GO annotation and KEGG annotation, 381 transcripts of 66 961 transcripts were related to the perception, transmission and light regulation of light signals, including red and far-red light receptor proteins PHYA, PHYB and signal pathway proteins PIF3, ELF3, blue light receptor proteins CRY, ZTL and signal pathway proteins COP1, SPA1, ELF3, GI, HY5, etc. The pathways related to plant pigment synthesis, such as flavonoid (including anthocyanin) metabolism, chlorophyll synthesis and carotenoid synthesis, contained 187 transcripts, 44 transcripts and 72 transcripts, respectively. A total of 2 079 transcription factors were obtained from the full-length transcripts, including 18 R2R3MYB transcription factors related to anthocyanin synthesis encoded by 35 transcripts. The number of long non-coding RNAs (LncRNAs) simultaneously annotated in the CNCI, CPC, Pfam, and PLEK databases was 6 359, which was higher than that of other bamboo species such as Xiaoshun bamboo. In this study, we obtained high-quality full-length transcriptome data, red and blue light receptors and light signal transduction proteins related to bamboo discoloration, and transcription factors and LncRNAs related to anthocyanin, chlorophyll and carotenoid synthesis, which provided a basis for further analysis of the mechanism of bamboo discoloration.

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备注/Memo

备注/Memo:
收稿日期：2023-11-27基金项目：国家重点研发计划项目(2023YFD2201901)作者简介：邵欣瑜(1999-),男,江苏南通人,硕士研究生,主要从事竹林培育研究。(E-mail)593376785@qq.com通讯作者：刘昌来,(E-mail)lcl2012@njfu.edu.cn；刘国华,(E-mail)ghliu@njfu.edu.cn
更新日期/Last Update: 2024-05-20