Genomic Analysis of LEA Genes in Carica papaya and Insight into Lineage-Specific Family Evolution in Brassicales.
Genomic Analysis of LEA Genes in Carica papaya and Insight into Lineage-Specific Family Evolution in Brassicales.
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DOI：
10.3390/life12091453
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发表时间：
2022-09-19
期刊：
影响因子：
--
通讯作者：
Guo A
中科院分区：
文献类型：
--
作者：
Zou Z;Guo J;Zheng Y;Xiao Y;Guo A
胚胎发育晚期丰蛋白（LEA）是一个参与植物发育和胁迫反应的多种蛋白超家族。木瓜是一种广泛种植于热带和亚热带地区的重要经济果树作物，本研究首次对木瓜LEA基因进行了全基因组分析。从木瓜基因组中鉴定出28个成员，分别属于8个家族，分别为LEA_1(3)、LEA_2(4)、LEA_3(5)、LEA_4(5)、LEA_5(2)、LEA_6(2)、DHN(4)和SMP(3)。其科数与蓖麻科（大戟科，28）和辣木科（辣木科，29）的科数相当，但与辣木科（Cleomaceae, 39）和拟南芥（芸苔科，51）的科数相对较少，暗示在芸苔科中存在谱系特异性进化。事实上，基于最佳往复命中的序列比较和同源性分析揭示了29个正群的存在，Tarenaya和拟南芥中显著的基因扩增主要是由于它们与木瓜分离后发生的全基因组复制。虽然也观察到转置复制的作用，但串联复制被证明是大多数物种基因扩增的关键贡献者。进一步的外显子-内含子结构和蛋白质基序的比较分析支持了这一特殊超家族的快速进化，特别是在拟南芥中。转录谱分析揭示了CpLEA基因在不同组织和不同发育阶段果实中的不同表达模式。此外，大多数基因的转录水平似乎受到干旱、寒冷和盐胁迫的显著调节，这与启动子区域中与胁迫反应相关的顺式作用元件的存在相对应。这些发现不仅提高了我们对芸苔科植物谱系特异性家族进化的认识，而且为进一步分析木瓜LEA基因的功能提供了有价值的信息。
Late embryogenesis abundant (LEA) proteins comprise a diverse superfamily involved in plant development and stress responses. This study presents a first genome-wide analysis of LEA genes in papaya (Carica papaya L., Caricaceae), an economically important tree fruit crop widely cultivated in the tropics and subtropics. A total of 28 members were identified from the papaya genome, which belong to eight families with defined Pfam domains, i.e., LEA_1 (3), LEA_2 (4), LEA_3 (5), LEA_4 (5), LEA_5 (2), LEA_6 (2), DHN (4), and SMP (3). The family numbers are comparable to those present in Ricinus communis (Euphorbiaceae, 28) and Moringa oleifera (Moringaceae, 29), but relatively less than that found in Moringa oleifera (Cleomaceae, 39) and Arabidopsis thaliana (Brassicaceae, 51), implying lineage-specific evolution in Brassicales. Indeed, best-reciprocal-hit-based sequence comparison and synteny analysis revealed the presence of 29 orthogroups, and significant gene expansion in Tarenaya and Arabidopsis was mainly contributed by whole-genome duplications that occurred sometime after their split with the papaya. Though a role of transposed duplication was also observed, tandem duplication was shown to be a key contributor in gene expansion of most species examined. Further comparative analyses of exon-intron structures and protein motifs supported fast evolution of this special superfamily, especially in Arabidopsis. Transcriptional profiling revealed diverse expression patterns of CpLEA genes over various tissues and different stages of developmental fruit. Moreover, the transcript level of most genes appeared to be significantly regulated by drought, cold, and salt stresses, corresponding to the presence of cis-acting elements associated with stress response in their promoter regions. These findings not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further functional analysis of LEA genes in papaya.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
转录组学和共表达网络揭示了木瓜中轻度和严重干旱的组织特异性响应和调节中心（Carica Papaya L.）。
影响因子：
4.6
作者：
Gamboa-Tuz SD;Pereira-Santana A;Zamora-Briseño JA;Castano E;Espadas-Gil F;Ayala-Sumuano JT;Keb-Llanes MÁ;Sanchez-Teyer F;Rodríguez-Zapata LC
通讯作者：
Rodríguez-Zapata LC
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS
影响因子：
7.4
作者：
Battaglia, Marina;Olvera-Carrillo, Yadira;Covarrubias, Alejandra A.
通讯作者：
Covarrubias, Alejandra A.
影响因子：
12.3
作者：
Jiao Y;Leebens-Mack J;Ayyampalayam S;Bowers JE;McKain MR;McNeal J;Rolf M;Ruzicka DR;Wafula E;Wickett NJ;Wu X;Zhang Y;Wang J;Zhang Y;Carpenter EJ;Deyholos MK;Kutchan TM;Chanderbali AS;Soltis PS;Stevenson DW;McCombie R;Pires JC;Wong GK;Soltis DE;Depamphilis CW
通讯作者：
Depamphilis CW