Identification and characterization of the abscisic acid (ABA) receptor gene family and its expression in response to hormones in the rubber tree

Guo, Dong; Zhou, Ying; Li, Hui‐Liang; Zhu, Jiahong; Wang, Ying; Xiong-ting, Chen; Peng, Shi-Qing

doi:10.1038/srep45157

Cited by 38 publications

(40 citation statements)

References 47 publications

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“…ABA receptor PYLs are key regulators of ABA signaling, and have been investigated in many plants in recent years ( Boneh et al, 2012 ; Kim et al, 2012 ; Bai et al, 2013 ; González-Guzmán et al, 2014 ; Fan et al, 2016 ; Gordon et al, 2016 ; Zhang et al, 2015 ; Chen et al, 2017 ; Guo et al, 2017 ; Liang et al, 2017 ). However, knowledge about phylogenesis and the roles of most PYLs in Gossypium is limited.…”

Section: Discussionmentioning

confidence: 99%

“… Liang et al (2017) also found that cotton GhPYL9-11A positively regulate drought tolerance in transgenic Arabidopsis plants. In recent years, many PYL gene families have been characterized at genome-wide levels in rice, grape, soybean and other plants ( Boneh et al, 2012 ; Kim et al, 2012 ; Bai et al, 2013 ; González-Guzmán et al, 2014 ; Tian et al, 2015 ; Fan et al, 2016 ; Gordon et al, 2016 ; Yu et al, 2016 ; Guo et al, 2017 ; Zhang et al, 2017 ). Furthermore, the structure properties of AtPYLs in Arabidopsis have been intensively investigated.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification of ABA receptor PYL family and expression analysis of PYLs in response to ABA and osmotic stress in Gossypium

Zhang

Miao

et al. 2017

PeerJ

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Abscisic acid (ABA) receptor pyrabactin resistance1/PYR1-like/regulatory components of ABA receptor (PYR1/PYL/RCAR) (named PYLs for simplicity) are core regulators of ABA signaling, and have been well studied in Arabidopsis and rice. However, knowledge is limited about the PYL family regarding genome organization, gene structure, phylogenesis, gene expression and protein interaction with downstream targets in Gossypium. A comprehensive analysis of the Gossypium PYL family was carried out, and 21, 20, 40 and 39 PYL genes were identified in the genomes from the diploid progenitor G. arboretum, G. raimondii and the tetraploid G. hirsutum and G. barbadense, respectively. Characterization of the physical properties, chromosomal locations, structures and phylogeny of these family members revealed that Gossypium PYLs were quite conservative among the surveyed cotton species. Segmental duplication might be the main force promoting the expansion of PYLs, and the majority of the PYLs underwent evolution under purifying selection in Gossypium. Additionally, the expression profiles of GhPYL genes were specific in tissues. Transcriptions of many GhPYL genes were inhibited by ABA treatments and induced by osmotic stress. A number of GhPYLs can interact with GhABI1A or GhABID in the presence and/or absence of ABA by the yeast-two hybrid method in cotton.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of ABA receptor PYL family and expression analysis of PYLs in response to ABA and osmotic stress in Gossypium

Zhang

Miao

et al. 2017

PeerJ

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“…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).…”

Section: Pendahuluanunclassified

“…LTP dapat ditemukan secara luas di berbagai organisme dengan fungsi dan ukuran yang bervariasi (Wang et al, 2012). Chen et al, (2017) melaporkan bahwa LTP terlibat dalam respon cekaman abiotik berupa suhu rendah dan kekeringan pada tanaman tebu. LTP juga berperan dalam toleransi suhu tinggi pada tanaman gandum (Yu et al, 2014).…”

Section: Identifikasi Domain Dan Familiunclassified

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)

Martiansyah¹,

Putranto²,

Khumaida³

2017

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Protease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].

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“…However, this technique requires the advances on genetics and genomics. Recent progress in next-generation sequencing technique greatly promoted the genomic study in rubber tree [4][5][6][7][8][9][10][11][12][13]. At current stage, 4 versions of draft genome in rubber trees were compiled [14][15][16][17] and more than 100 NGS transcriptomic data were produced [18][19][20][21][22][23][24][25].…”

mentioning

confidence: 99%

HeveaDB: a genetic resource database for rubber tree genomic study

Cheng

Xia

Zhou

et al. 2019

Preprint

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With the proceedings in the genome study in rubber tree, more and more data were produced. However, these data are still deposited in public databases as raw format, and the utilization of these NGS data is hindered for the researchers in rubber tree community. HeveaDB was therefore constructed and maintained under the organization of International Rubber Research and Development Board. The HeveaDB 1.0 (http://hevea.catas.cn) mainly stores 4 versions of Hevea draft genome, 99 NGS transcriptomes, 18451annotated EST sequences, 12 curated gene families, 30200 gene annotations, 5049 wild germplasm phenotype data, and 18328 Wickham rubber clonal information. Several bioinformatic tools are integrated in the database to facilitate the utilization of the data for the users who are not skilled in bioinformatics.With the periodical update and functional improvement, the HeveaDB will serve as a potential platform for genomic studies and breeding technology in rubber tree.

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Identification and characterization of the abscisic acid (ABA) receptor gene family and its expression in response to hormones in the rubber tree

Cited by 38 publications

References 47 publications

Genome-wide identification of ABA receptor PYL family and expression analysis of PYLs in response to ABA and osmotic stress in Gossypium

Genome-wide identification of ABA receptor PYL family and expression analysis of PYLs in response to ABA and osmotic stress in Gossypium

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)

HeveaDB: a genetic resource database for rubber tree genomic study

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