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Vaishali Khanale
Mahyco Private Limited
Corresponding Author
ORCiD: https://orcid.org/0000-0001-8013-2537
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Cotton is an important commodity in the world economy. In this study we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species G. hirsutum along with two sub-genome species of allotetraploid cotton, G. arboreum and G. raimondii. A total of 228 bZIP genes of G. hirsutum, 91 bZIP genes of G. arboreum and 86 bZIP genes of G. raimondii were identified from CottonGen database. Cotton bZIP genes were annotated in standard pattern according to their match with Arabidopsis bZIPs. Multiple genes with similar bZIP designations were observed in cotton, linked to the gene duplication. Cotton bZIPs are distributed across all 13 chromosomes with varied density. Phylogenetic characterization of all three cotton species bZIPs classified them into 12 subfamilies, namely A B, C, D, E, F, G, H, I, J, K and S and further into eight subgroups according to their predicted functional similarities, viz., A1, A2, A3, C1, C2, S1, S2 and S3. Subfamily A and S are having maximum number of bZIP genes, subfamily B, H, J and K are single member families. Cotton bZIP protein functions were predicted from identified motifs and orthologs from varied species. BRLZ domain analysis of G. raimondii bZIPs revealed the presence of conserved basic region motif N-X7-R/K in almost all subfamily members, variants are GrbZIP62 with N-X7-I motif and GrbZIP76 with K-X7-R motif. Leucine heptad repeats motif, are also present in variant numbers from two to nine with leucine or other hydrophobic amino acid at designated position among 12 subfamily members. STRING protein interaction network analysis of G. raimondii bZIPs observed strong interaction between A-D, B-K and C-S subfamily members.
Keywords
G. hirsutum, G. arboreum, G. raimondii, bZIP proteins, plant development, stress adaptation
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- Tables.pdf
Tables 1 - 4
- Onlineresource1.xlsx
1] Supplementary file 1 –Xls. (Online resource 1) All identified bZIP gene ID, exon number, CDS length, protein length and protein sequences of G. hirsutum, G. arboreum and G. raimondii. G. hirsutum, G. arboreum and G. raimondii bZIP34, bZIP61, bZIP69 and bZIP76 protein alignment.
- MASTfor4Ghand1GrremainingbZIPs1.html
2] MEME motif analysis MAST files of G. hirsutum, G. arboreum and G. raimondii bZIP proteins
- MASTGrbZIPsselectedonly1stGeneofeachbZIPs2.html
2] MEME motif analysis MAST files of G. hirsutum, G. arboreum and G. raimondii bZIP proteins
- Supplimentarygammadistributionphylotree.png
3] Gamma distribution phylogenetic tree
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Vaishali Khanale
Mahyco Private Limited
Corresponding Author
ORCiD: https://orcid.org/0000-0001-8013-2537
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 06 Apr, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Cotton is an important commodity in the world economy. In this study we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species G. hirsutum along with two sub-genome species of allotetraploid cotton, G. arboreum and G. raimondii. A total of 228 bZIP genes of G. hirsutum, 91 bZIP genes of G. arboreum and 86 bZIP genes of G. raimondii were identified from CottonGen database. Cotton bZIP genes were annotated in standard pattern according to their match with Arabidopsis bZIPs. Multiple genes with similar bZIP designations were observed in cotton, linked to the gene duplication. Cotton bZIPs are distributed across all 13 chromosomes with varied density. Phylogenetic characterization of all three cotton species bZIPs classified them into 12 subfamilies, namely A B, C, D, E, F, G, H, I, J, K and S and further into eight subgroups according to their predicted functional similarities, viz., A1, A2, A3, C1, C2, S1, S2 and S3. Subfamily A and S are having maximum number of bZIP genes, subfamily B, H, J and K are single member families. Cotton bZIP protein functions were predicted from identified motifs and orthologs from varied species. BRLZ domain analysis of G. raimondii bZIPs revealed the presence of conserved basic region motif N-X7-R/K in almost all subfamily members, variants are GrbZIP62 with N-X7-I motif and GrbZIP76 with K-X7-R motif. Leucine heptad repeats motif, are also present in variant numbers from two to nine with leucine or other hydrophobic amino acid at designated position among 12 subfamily members. STRING protein interaction network analysis of G. raimondii bZIPs observed strong interaction between A-D, B-K and C-S subfamily members.
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- Tables.pdf
Tables 1 - 4
- Onlineresource1.xlsx
1] Supplementary file 1 –Xls. (Online resource 1) All identified bZIP gene ID, exon number, CDS length, protein length and protein sequences of G. hirsutum, G. arboreum and G. raimondii. G. hirsutum, G. arboreum and G. raimondii bZIP34, bZIP61, bZIP69 and bZIP76 protein alignment.
- MASTfor4Ghand1GrremainingbZIPs1.html
2] MEME motif analysis MAST files of G. hirsutum, G. arboreum and G. raimondii bZIP proteins
- MASTGrbZIPsselectedonly1stGeneofeachbZIPs2.html
2] MEME motif analysis MAST files of G. hirsutum, G. arboreum and G. raimondii bZIP proteins
- Supplimentarygammadistributionphylotree.png
3] Gamma distribution phylogenetic tree
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