A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

Abstract

BackgroundSmall auxin-up RNA (SAUR) gene family is the largest family of early auxin response genes in higher plants, which have been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in cotton (Gossypium spp.).ResultsIn the study, we identified 145, 97, 214, and 176 SAUR homologous genes in the sequenced genomes of G. raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. A phylogenetic analysis revealed that the SAUR genes can be classified into 10 groups. A further analysis of chromosomal locations and gene duplications showed that tandem duplication and segmental duplication events contributed to the expansion of the SAUR gene family in cotton. An exon-intron organization and motif analysis revealed the conservation of SAUR-specific domains, and the auxin responsive elements existed in most of the upstream sequences. The expression levels of 16 GhSAUR genes in response to an exogenous application of IAA were determined by a quantitative RT-PCR analysis. The genome-wide RNA-seq data and qRT-PCR analysis of selected SAUR genes in developing fibers revealed their differential expressions. The physical mapping showed that 20 SAUR genes were co-localized with fiber length quantitative trait locus (QTL) hotspots. Single nucleotide polymorphisms (SNPs) were detected for 12 of these 20 genes between G. hirsutum and G. barbadense, but no SNPs were identified between two backcross inbred lines with differing fiber lengths derived from a cross between the two cultivated tetraploids.ConclusionsThis study provides an important piece of genomic information for the SAUR genes in cotton and lays a solid foundation for elucidating the functions of SAUR genes in auxin signaling pathways to regulate cotton growth.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4224-2) contains supplementary material, which is available to authorized users.

Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)

“…Multiple alignment of all the predicted PEL protein sequences from the three Gossypium species, Arabidopsis , Corchorus olitorius , Theobroma cacao , Oryza sativa and Populus genomes was performed using ClustalX 2.0 [ 60 ]. An unrooted phylogenetic tree was generated using the neighbor-joining (NJ) method and the amino acid p-distance model in MEGA 6.0 [ 61 ].…”

A Pivotal Role of Hormones in Regulating Cotton Fiber Development

“…All members of AGAMOUS subfamily were significantly induced by auxin (Moura et al., 2016). The expression levels of most GhSAUR genes are responsive to exogenous application of IAA treatment (Li et al., 2017).…”

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

“…The predicted SWEET proteins were first aligned by ClustalW 2.0 at EMBL-EBI (http://www.ebi.ac.uk/Tools/msa/clustalw2/) prior to a gene duplication analysis. Gene duplication events were defined according to the following conditions: the alignment region covered more than 80% of the longer gene and the identity of the aligned regions was over 80% (Li et al 2017). The collinearity pairs of SWEET family were mapped using Circos software (Krzywinski et al 2009).…”