A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development

Phalaenopsis has a zygomorphic floral structure, including three outer tepals, two lateral inner tepals and a highly modified inner median tepal called labellum or lip; however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for fl...

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Veröffentlicht in:PloS one 2015-05, Vol.10 (5), p.e0123474-e0123474
Hauptverfasser: Huang, Jian-Zhi, Lin, Chih-Peng, Cheng, Ting-Chi, Chang, Bill Chia-Han, Cheng, Shu-Yu, Chen, Yi-Wen, Lee, Chen-Yu, Chin, Shih-Wen, Chen, Fure-Chyi
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container_issue 5
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container_title PloS one
container_volume 10
creator Huang, Jian-Zhi
Lin, Chih-Peng
Cheng, Ting-Chi
Chang, Bill Chia-Han
Cheng, Shu-Yu
Chen, Yi-Wen
Lee, Chen-Yu
Chin, Shih-Wen
Chen, Fure-Chyi
description Phalaenopsis has a zygomorphic floral structure, including three outer tepals, two lateral inner tepals and a highly modified inner median tepal called labellum or lip; however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for floral organs of the Phalaenopsis wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after de novo assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression. PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes' expression patterns. PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. Our study provides new insights into how the orchid labellum differs and why the petal or sepal converts to a labellum in Phalaenopsis floral mutants.
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We generated RNA-seq reads with the Illumina platform for floral organs of the Phalaenopsis wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after de novo assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression. PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes' expression patterns. PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. 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PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. 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histology</subject><subject>Orchidaceae - classification</subject><subject>Orchidaceae - genetics</subject><subject>Orchidaceae - growth &amp; development</subject><subject>Organ Specificity</subject><subject>Organs</subject><subject>Oryza</subject><subject>Petals</subject><subject>Phylogeny</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Science</subject><subject>Sepals</subject><subject>Transcription</subject><subject>Transcription factors</subject><subject>Transcriptome</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptUl1rFDEUDaLYuvoPRAO--LJrPu5kNi9CKVULBX1Q8C1kMne6s2SSMZnd4r9vtjstrUgeEpJzTs65HELecrbisuaftnGXgvWrMQZcMS4k1PCMnHItxVIJJp8_Op-QVzlvGavkWqmX5ERUumZVLU7J7zPaIg1xH2nnY7KeTsmG7FI_TnFAmnCP1mfq_A4z7cMU6Y-N9RZDHHOfaUxu07cH7g2mIrVHH8cBw_SavOgKEd_M-4L8-nLx8_zb8ur718vzs6ulq4SalmgdoGQMK2CNxMYhdFBZx4RijqEFaa3qFCjWtBqca0A1SmvoZNMxACYX5P1Rd_Qxm3ko2XC1ZnVZWhbE5RHRRrs1Y-oHm_6aaHtzdxHTtbFp6p1H02rRaOR8LWoFoJWWSgrRVKqDtuZFbEE-z7_tmgFbV4KWmT0RffoS-o25jnsDIBmsD3Y_zgIp_ikjnczQZ4fe24Bxd-ebCyW5hAL98A_0_-ngiHIp5pywezDDmTkU5Z5lDkUxc1EK7d3jIA-k-2bIWzMrvIQ</recordid><startdate>20150513</startdate><enddate>20150513</enddate><creator>Huang, Jian-Zhi</creator><creator>Lin, Chih-Peng</creator><creator>Cheng, Ting-Chi</creator><creator>Chang, Bill Chia-Han</creator><creator>Cheng, Shu-Yu</creator><creator>Chen, Yi-Wen</creator><creator>Lee, Chen-Yu</creator><creator>Chin, Shih-Wen</creator><creator>Chen, Fure-Chyi</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150513</creationdate><title>A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development</title><author>Huang, Jian-Zhi ; 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however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for floral organs of the Phalaenopsis wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after de novo assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression. PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes' expression patterns. PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. Our study provides new insights into how the orchid labellum differs and why the petal or sepal converts to a labellum in Phalaenopsis floral mutants.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25970572</pmid><doi>10.1371/journal.pone.0123474</doi><oa>free_for_read</oa></addata></record>
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subjects Antirrhinum
Antirrhinum majus
Arabidopsis
Arabidopsis thaliana
Contig Mapping
Dendrobium
Flowers
Flowers & plants
Flowers - anatomy & histology
Flowers - genetics
Flowers - growth & development
Flowers - metabolism
Functional analysis
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Genes
High-Throughput Nucleotide Sequencing
Lip
Molecular Sequence Annotation
Morphology
Mutants
Mutation
Oncidium
Orchidaceae
Orchidaceae - anatomy & histology
Orchidaceae - classification
Orchidaceae - genetics
Orchidaceae - growth & development
Organ Specificity
Organs
Oryza
Petals
Phylogeny
Plant Proteins - genetics
Plant Proteins - metabolism
Ribonucleic acid
RNA
Science
Sepals
Transcription
Transcription factors
Transcriptome
title A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development
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