Transcriptome Sequencing and Differential Gene Expression Analysis of Delayed Gland Morphogenesis in Gossypium Australe During Seed Germination

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Sep 28

PMID 24073262

Citations 17

Authors

Tao Tao

Liang Zhao

Yuanda Lv

Jiedan Chen

Yan Hu

Tianzhen Zhang

Baoliang Zhou

Affiliations

Soon will be listed here.

Abstract

The genus Gossypium is a globally important crop that is used to produce textiles, oil and protein. However, gossypol, which is found in cultivated cottonseed, is toxic to humans and non-ruminant animals. Efforts have been made to breed improved cultivated cotton with lower gossypol content. The delayed gland morphogenesis trait possessed by some Australian wild cotton species may enable the widespread, direct usage of cottonseed. However, the mechanisms about the delayed gland morphogenesis are still unknown. Here, we sequenced the first Australian wild cotton species (Gossypiumaustrale) and a diploid cotton species (Gossypiumarboreum) using the Illumina Hiseq 2000 RNA-seq platform to help elucidate the mechanisms underlying gossypol synthesis and gland development. Paired-end Illumina short reads were de novo assembled into 226,184, 213,257 and 275,434 transcripts, clustering into 61,048, 47,908 and 72,985 individual clusters with N50 lengths of 1,710 bp, 1544 BP and 1,743 bp, respectively. The clustered Unigenes were searched against three public protein databases (TrEMBL, SwissProt and RefSeq) and the nucleotide and protein sequences of Gossypiumraimondii using BLASTx and BLASTn. A total of 21,987, 17,209 and 25,325 Unigenes were annotated. Of these, 18,766 (85.4%), 14,552 (84.6%) and 21,374 (84.4%) Unigenes could be assigned to GO-term classifications. We identified and analyzed 13,884 differentially expressed Unigenes by clustering and functional enrichment. Terpenoid-related biosynthesis pathways showed differentially regulated expression patterns between the two cotton species. Phylogenetic analysis of the terpene synthases family was also carried out to clarify the classifications of TPSs. RNA-seq data from two distinct cotton species provide comprehensive transcriptome annotation resources and global gene expression profiles during seed germination and gland and gossypol formation. These data may be used to further elucidate various mechanisms and help promote the usage of cottonseed.

Citing Articles

Identification of MYB gene family and functional analysis of GhMYB4 in cotton (Gossypium spp.).

Dai Y, Liu S, Zuo D, Wang Q, Lv L, Zhang Y Mol Genet Genomics. 2023; 298(3):755-766.

PMID: 37027022 DOI: 10.1007/s00438-023-02005-5.

Comparative Transcriptome Analysis Reveals Genes Associated with the Gossypol Synthesis and Gland Morphogenesis in .

Zhang C, Liu X, Song Y, Sun Z, Zhang J, Wu H Genes (Basel). 2022; 13(8).

PMID: 36011363 PMC: 9408450. DOI: 10.3390/genes13081452.

Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean.

Bhat J, Karikari B, Adeboye K, Ganie S, Barmukh R, Hu D Theor Appl Genet. 2022; 135(7):2407-2422.

PMID: 35639109 PMC: 9271120. DOI: 10.1007/s00122-022-04120-0.

An Overview of Cotton Gland Development and Its Transcriptional Regulation.

Jan M, Liu Z, Guo C, Zhou Y, Sun X Int J Mol Sci. 2022; 23(9).

PMID: 35563290 PMC: 9103798. DOI: 10.3390/ijms23094892.

Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Infection Resulting in Reduced Aflatoxin Production in Groundnut.

Soni P, Nayak S, Kumar R, Pandey M, Singh N, Sudini H J Fungi (Basel). 2020; 6(4).

PMID: 33339393 PMC: 7767264. DOI: 10.3390/jof6040370.

References

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

Zhao Q, Wang Y, Kong Y, Luo D, Li X, Hao P . Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics. 2012; 12 Suppl 14:S2. PMC: 3287467. DOI: 10.1186/1471-2105-12-S14-S2. View

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

Saldanha A . Java Treeview--extensible visualization of microarray data. Bioinformatics. 2004; 20(17):3246-8. DOI: 10.1093/bioinformatics/bth349. View

Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N . TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003; 34(2):374-8. DOI: 10.2144/03342mt01. View

Martin G, Liu J, Benedict C, Stipanovic R, Magill C . Reduced levels of cadinane sesquiterpenoids in cotton plants expressing antisense (+)-delta-cadinene synthase. Phytochemistry. 2002; 62(1):31-8. DOI: 10.1016/s0031-9422(02)00432-6. View

Chen X, Wang M, Chen Y, Davisson V, Heinstein P . Cloning and heterologous expression of a second (+)-delta-cadinene synthase from Gossypium arboreum. J Nat Prod. 1996; 59(10):944-51. DOI: 10.1021/np960344w. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

10.

Waterhouse A, Procter J, Martin D, Clamp M, Barton G . Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25(9):1189-91. PMC: 2672624. DOI: 10.1093/bioinformatics/btp033. View

11.

Martin J, Wang Z . Next-generation transcriptome assembly. Nat Rev Genet. 2011; 12(10):671-82. DOI: 10.1038/nrg3068. View

12.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

13.

Roberts A, Pachter L . Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods. 2012; 10(1):71-3. PMC: 3880119. DOI: 10.1038/nmeth.2251. View

14.

Chen X, Chen Y, Heinstein P, Davisson V . Cloning, expression, and characterization of (+)-delta-cadinene synthase: a catalyst for cotton phytoalexin biosynthesis. Arch Biochem Biophys. 1995; 324(2):255-66. DOI: 10.1006/abbi.1995.0038. View

15.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

16.

Garber M, Grabherr M, Guttman M, Trapnell C . Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011; 8(6):469-77. DOI: 10.1038/nmeth.1613. View

17.

Benedict C, Liu J, Stipanovic R . The peroxidative coupling of hemigossypol to (+)- and (-)-gossypol in cottonseed extracts. Phytochemistry. 2006; 67(4):356-61. DOI: 10.1016/j.phytochem.2005.11.015. View

18.

Blackstaffe L, Shelley M, FISH R . Cytotoxicity of gossypol enantiomers and its quinone metabolite gossypolone in melanoma cell lines. Melanoma Res. 1998; 7(5):364-72. DOI: 10.1097/00008390-199710000-00002. View

19.

Bateman A, Coin L, Durbin R, Finn R, Hollich V, Griffiths-Jones S . The Pfam protein families database. Nucleic Acids Res. 2003; 32(Database issue):D138-41. PMC: 308855. DOI: 10.1093/nar/gkh121. View

20.

Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L . Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol. 2011; 29(8):762-6. DOI: 10.1038/nbt.1926. View