Genome-wide identification of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes and their response to ethephon stimulation in the laticifer, a rubber-producing tissue

Abstract

BackgroundNatural rubber, an important industrial raw material, is specifically synthesized in laticifers located inside the rubber tree (Hevea brasiliensis Muell. Arg.) trunk. Due to the absence of plasmodesmata, the laticifer water balance is mediated by aquaporins (AQPs). However, to date, the characterization of H. brasiliensis AQPs (HbAQPs) is still in its infancy.ResultsIn this study, 51 full-length AQP genes were identified from the rubber tree genome. The phylogenetic analysis assigned these AQPs to five subfamilies, including 15 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 9 NOD26-like intrinsic proteins (NIPs), 4 small basic intrinsic proteins (SIPs) and 6 X intrinsic proteins (XIPs). Functional prediction based on the analysis of the aromatic/arginine (ar/R) selectivity filter, Froger’s positions and specificity-determining positions (SDPs) showed a remarkable difference in substrate specificity among subfamilies. Homology analysis supported the expression of 44 HbAQP genes in at least one of the examined tissues. Furthermore, deep sequencing of the laticifer transcriptome in the form of latex revealed a key role of several PIP subfamily members in the laticifer water balance, and qRT-PCR analysis showed diverse expression patterns of laticifer-expressed HbAQP genes upon ethephon treatment, a widely-used practice for the stimulation of latex yield.ConclusionsThis study provides an important genetic resource of HbAQP genes, which will be useful to improve the water use efficiency and latex yield of Hevea.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2152-6) contains supplementary material, which is available to authorized users.

The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles

“…In this respect, EgTIP2.1, EgTIP2.2, and EgTIP4.1 have the same H residue in loop C as AtTIP2.1. Comparatively, several TIP2 orthologs from other plant species also have an AtTIP2.1-like extended selectivity filter (Zou et al, 2015a,b, 2016), thus suggesting that these proteins may be able to transport ammonia. Moreover, in view of the predictions for non-aqua transport profiles proposed by Azad et al (2016), both EgTIP2 and EgTIP4.1 as well as all EgTIP1 fulfill the requirements to act as H 2 O 2 transporters.…”

“…In A. thaliana , the TIP subfamily is composed of 10 members that are phylogenetically classified into five subgroups (Johanson et al, 2001). In forest and fruit tree species, genome-wide surveys revealed the presence of 17 TIP genes in Populus trichocarpa (Gupta and Sankararamakrishnan, 2009) and Hevea brasiliensis (Zou et al, 2015a), while 10 and 11 genes were identified in Vitis vinifera and Citrus sinensis , respectively (Shelden et al, 2009; Martins et al, 2015). Intriguingly, a preliminary study identified a relatively small number of TIP genes (five in total) in the Eucalyptus genome (Rodrigues et al, 2013).…”

Pemanfaatan bioinformatika dalam bidang pertanian dan kesehatan (The utilization of bioinformatics in the field of agriculture and health)

“…Pada skala yang lebih besar, alur kerja (workflow) dan skema (pipeline) bioinformatika juga telah membantu berbagai analisis transkriptomik dan genomik pada tanaman perkebunan seperti identifikasi famili gen penting (Liu et al, 2016, Dou et al, 2014, Duan et al, 2013, studi asosiasi gen (Teh et al, 2016;Liu et al, 2016;Zou et al, 2015;Dou et al, 2014;Duan et al, 2013;Ting et al, 2013), identifikasi SNP (Zhou et al, 2016, dan identifikasi QTL (Ting et al, 2013). Skema kerja dari CIRAD, Prancis yang disebut basis data ESTtik (http://esttik.cirad.fr/) telah berhasil digunakan untuk mengidentifikasi superfamili APETALA2 /ETHYLENE RESPONSE FACTORS (AP2/ERF) pada tanaman karet dari hasil sekuensing dengan teknologi Whole Genome Sequencing Roche 454 (Duan et al, 2013).…”

“…Basis data lncRNABase merupakan kumpulan dari 108 data CLIP-Seq terutama pada mamalia dan cacing (Li et al, 2014). Basis data ChiPBase merupakan anotasi dari profil ekspresi lncRNAs dan ncRNAs dari 10.200 ChIPseq data (Yang et al, 2015). LNCipedia merupakan basis data anotasi dari 21.448 transkrip lncRNAs pada manusia (Volders et al, 2013).…”

Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

“…Identifikasi gen spesifik dan fungsinya membantu kita dalam memahami perkembangan evolusi molekuler gen dan protein serta lebih jauh lagi dapat mengenali perbedaan morfologi ataupun fenotipe tanaman (Sharma & Suresh, 2015). Analisis in silico komparatif A. thaliana dan H. brasiliensis telah berhasil mengidentifikasi beberapa famili gen penting seperti superfamili APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERF) (Duan et al, 2010;Putranto & Montoro, 2016;Putranto et al, 2015a;Putranto et al, 2015b) famili CalciumDependent Protein Kinase (CDPK) (Xiao et al, 2017), famili reseptor asam absisat (ABA) (Guo et al, 2017), famili Glucose-6-Phosphate Dehydrogenase (G6PDH) , famili Metacaspase , famili Aquaporin (Zou et al, 2015), dan famili ABC Transporter (Zhiyi et al, 2015). Di sisi lain, studi komparatif sejenis juga telah berhasil dilakukan pada spesies lain seperti Oryza vs Shorgum untuk identifikasi dan analisis filogenetik gen transporter Ca 2+ (Goel et al, 2011) dan gen siDof pada tanaman millet (Setaria italica) ( Zhang et al, 2017).…”