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Open Access Research article

Characterization of expressed sequence tags from developing fibers of Gossypium barbadense and evaluation of insertion-deletion variation in tetraploid cultivated cotton species

Yuanda Lv, Liang Zhao, Xiaoyang Xu, Lei Wang, Cheng Wang, Tianzhen Zhang and Wangzhen Guo*

Author Affiliations

National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, China

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BMC Genomics 2013, 14:170  doi:10.1186/1471-2164-14-170

Published: 13 March 2013

Additional files

Additional file 1: Table S1:

Functional annotation and classification summary for 8653 unigenes. Note: These unigenes were submitted to nr (non-redundant) protein database and assigned with GO (Gene Ontology) and KO (KEGG) terms.

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Additional file 2: Table S2:

Statistic analysis of KEGG classification with corresponding metabolism maps. Note: KO (KEGG) annotation and metabolism maps were performed with BLAST2GO. Classification showed in second level and third level.

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Additional file 3: Figure S1:

Experimental verification of candidate unigenes expressed specifically in G. barbadense using RT-PCR.

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Additional file 4: Table S3:

Function annotation of 408 putative G. barbadense -specific unigenes. Note: 408 unigenes without significant match to any sequence in the current G. hirsutum EST databases were identified and finished function annotation against nr (non-redundant) protein database.

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Additional file 5: Table S4:

Summary for putative Gb-Gh Indel loci by in silic analysis. Notes: The information on insert size both in G. barbadense (Gb) and G. hirsutum (Gh), and size range was supplied in the table.

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Additional file 6: Table S5:

2,160 Indel markers developed by using InDel > =5 bp EST sequences between G. barbadense and G. hirsutum.

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Additional file 7: Table S6:

PCR amplification and banding patterns of randomly selected 90 Indel markers. Note: 1: No difference in tested accessions; 3: showed orthologous and/or homoeologous loci polymorphism in tested accessions.

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Additional file 8: Table S7:

Function identification related to secondary wall synthesis using sequences detected InDels by tblastx analysis with databases from Arabidopsis.

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