中國農業科學 ?? 2020, Vol. 53 ?? Issue (5): 1004-1017.doi: 10.3864/j.issn.0578-1752.2020.05.012

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辣椒HD-Zip基因家族鑒定、系統進化及表達分析

邵晨冰,黃志楠,白雪瀅,王云鵬,段偉科()   

  1. 淮陰工學院生命科學與食品工程學院,江蘇淮安 223003
  • 收稿日期:2019-07-30 接受日期:2019-09-23 出版日期:2020-03-01 發布日期:2020-03-14
  • 通訊作者: 段偉科 E-mail:[email protected]
  • 作者簡介:邵晨冰,E-mail:[email protected]
  • 基金資助:
    江蘇省自然科學基金青年基金(BK20170462);國家自然科學基金青年科學基金(31701931);國家自然科學基金青年科學基金(31902021);淮陰工學院博士科研啟動基金(Z301B16547);淮陰工學院博士科研啟動基金(Z301B16548)

Identification, Systematic Evolution and Expression Analysis of HD-Zip Gene Family in Capsicum annuum

SHAO ChenBing,HUANG ZhiNan,BAI XueYing,WANG YunPeng,DUAN WeiKe()   

  1. College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, Jiangsu
  • Received:2019-07-30 Accepted:2019-09-23 Online:2020-03-01 Published:2020-03-14
  • Contact: WeiKe DUAN E-mail:[email protected]

摘要:

【目的】鑒定辣椒HD-Zip基因家族,并利用生物信息學方法系統分析其在基因組中的分布、基因結構、進化分化特征及在不同組織中的時空表達特異性,解析該家族的進化特征及生物學功能。【方法】根據已報道及PlantTFDB數據庫中的擬南芥HD-Zip序列,利用本地BLAST工具在我國辣椒測序品種‘遵辣1號’基因組中比對,并利用Pfam、SMART工具進一步驗證。采用EMBOSS Programs、MEGA、GSDS、MEME、MCScanX、OrthoMCL、Circos等軟件預測辣椒HD-Zip基因家族成員蛋白理化性質,構建系統進化樹,定位染色體,分析基因結構、基因復制類型及直系、旁系同源基因。基于GEO數據庫,運用R軟件、本地perl語言及Cytoscape分析辣椒HD-Zip組織表達差異并繪制共表達網絡。【結果】本研究在‘遵辣1號’基因組中鑒定獲得42條辣椒HD-Zip,命名為CaHDZ01—CaHDZ42CaHDZs長度跨度較大,70% CaHDZ蛋白的pI小于7.0。除CaHDZ42,其余基因不均勻地分布在12條染色體上,部分基因為片段復制。該基因家族可分為4個亞族,分別含有18、9、5、10個HD-Zip,基因結構及蛋白結構域差別顯著。辣椒、番茄和擬南芥3個物種中的直系同源基因對數目大體相同,但同為茄科的辣椒和番茄之間的稍多;辣椒中的旁系同源基因少于番茄和擬南芥,說明辣椒基因組的倍增事件并沒有使CaHDZs明顯擴增。對無油樟、水稻、玉米、番茄、馬鈴薯、辣椒‘CM334’、辣椒‘Zunla-1’、毛果楊、葡萄以及擬南芥9個代表物種的HD-Zip進化特征分析結果表明,從被子植物開始,HD-Zip基因家族就穩定存在4個亞族。推測在形成4個亞族前,HD-Zip分為兩組,其中一組分化成I和II亞族,而另一組則分化成為III和IV亞族。CaHDZs在根、莖、葉、花芽、花和果實不同發育時期的表達模式分析結果顯示,4個亞族具有不同程度的表達趨勢。其中I亞族基因在辣椒不同組織中的表達量均較高,且不同成員間表達模式不同,CaHDZ22在莖中的表達最高,表明該基因可能對辣椒莖的生長有重要作用。II、III和IV亞族基因在不同組織中的表達量相對較低,但部分基因在特定組織中具有較大的表達量。如CaHDZ34在辣椒果實成熟后期具有較大高的表達量,CaHDZ02CaHDZ28在果實膨大時表達較高,CaHDZ04在果實成熟前期具有較高的表達量。CaHDZs表達網絡中有33對基因表達趨勢的相關系數(PCC)大于0.8,6對大于0.9,表明CaHDZs協同調控了辣椒的生長發育,不同亞族之間也具有協同性。【結論】在‘遵辣1號’基因組中鑒定獲得42條CaHDZs,可分為4個亞族,不同亞族的基因結構、蛋白保守結構域及表達模式不同。在進化過程中,辣椒HD-Zip保守性高,數目沒有明顯擴增,I和II亞族、III和IV亞族關系更近。CaHDZs具有組織表達差異性,協同調控了辣椒的生長發育。

關鍵詞: 辣椒, HD-Zip基因家族, 系統進化, 表達分析

Abstract:

【Objective】The objectives of this research were to identify the Homeodomain-Leucine Zipper (HD-Zip) family genes from pepper (Capsicum annuum) genome, to know the profile of HD-Zip family such as gene number, gene distribution, gene structure, evolutionary process and expression patterns in different tissues, and to provide theoretical basis for exploring what roles the HD-Zips play in pepper. 【Method】HD-Zip genes in pepper genome were identified by BLAST software based on HD-Zip from Arabidopsis, and verified by Pfam and SMART software. EMBOSS Programs, MEGA, GSDS, MEME, MCScanX, OrthoMCL and Circos softwares were used for bioinformatics analysis of HD-Zip protein and gene sequences. Expression patterns and gene co-regulatory network were analyzed by R and Cytoscape software. 【Result】Total of 42 HD-Zip genes were identified from ‘Zunla-1’ pepper genome, named as CaHDZ01-CaHDZ42. The length of their coding sequences ranged from 459 to 2 529 bps, and the isoelectric point of 70% CaHDZs was less than 7.0. The analysis of the gene’s location on the chromosome revealed that CaHDZs were unevenly distributed on 12 chromosomes of the pepper, except for CaHDZ42. The gene family could be divided into four subgroups, containing 18, 9, 5 and 10 CaHDZ genes, respectively. There were significant differences in gene structure and protein conserved domains among the subgroups. The number of orthologs among pepper, tomato and Arabidopsis was almost the same, but there were a little more orthologs between pepper and tomato. While the number of paralogs in Arabidopsis was significantly more than that in tomato and pepper, and the least in pepper, suggesting that the number of CaHDZ genes did not increase significantly along with genomic replication. To further understand the evolutionary history of CaHDZs in plant, HD-Zip homologous genes in Arabidopsis and 8 other plant species were analyzed. The results showed that all the major subgroups of HD-Zips existed in angiosperms. It was inferred that HD-Zip genes were divided into two groups initially. Then, one group differentiated into subgroup I and II, and the other differentiated into subgroups III and IV. The results of expression patterns analysis showed that the expression trends of four subgroups were different. Most of subgroup I genes expressed highly in pepper, such as CaHDZ22, and the expression of which was highest in stem, suggesting that this gene might play an important role in the growth of pepper stem. The expressions of subgroups II, III and IV CaHDZs were relatively low, but some of them expressed highly in specific tissues. For example, the expression of CaHDZ34 was high in late ripening stage of pepper fruits, CaHDZ02 and CaHDZ28 expressed highly in fruit enlargement stage, and CaHDZ04 expressed highly in early ripening stage of pepper fruits. In the coregulatory networks of CaHDZs, the Pearson correlation coefficients (PCCs) of 33 pairs of CaHDZs were greater than 0.8, and 6 pairs were greater than 0.9, suggesting that the CaHDZs coordinated the growth and development in pepper, and there were cooperative interactions among subgroups. 【Conclusion】All of 42 HD-Zip gene family members were identified from the ‘Zunla-1’ pepper genome, which could be divided into four subgroups. During the evolutionary history, CaHDZs were highly conservative and expanded slowly. Subgroup I and subgroup II had a closer relationship, so did subgroup III and subgroup IV. CaHDZ genes expressed specifically in different tissues and coordinately regulated the growth and development of pepper.

Key words: Capsicum annuum, HD-Zip gene family, systematic evolution, gene expression analyses

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