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

Overview of attention for article published in BMC Genomics, October 2017
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Title
A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton
Published in
BMC Genomics, October 2017
DOI 10.1186/s12864-017-4224-2
Pubmed ID
Authors

Xihua Li, Guoyuan Liu, Yanhui Geng, Man Wu, Wenfeng Pei, Honghong Zhai, Xinshan Zang, Xingli Li, Jinfa Zhang, Shuxun Yu, Jiwen Yu

Abstract

Small 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.). In 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. This 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 36 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 36 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 22%
Student > Master 3 8%
Other 2 6%
Student > Doctoral Student 2 6%
Student > Bachelor 2 6%
Other 6 17%
Unknown 13 36%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 33%
Biochemistry, Genetics and Molecular Biology 6 17%
Environmental Science 1 3%
Unspecified 1 3%
Pharmacology, Toxicology and Pharmaceutical Science 1 3%
Other 0 0%
Unknown 15 42%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 October 2017.
All research outputs
#17,918,662
of 23,006,268 outputs
Outputs from BMC Genomics
#7,612
of 10,693 outputs
Outputs of similar age
#234,557
of 327,882 outputs
Outputs of similar age from BMC Genomics
#139
of 211 outputs
Altmetric has tracked 23,006,268 research outputs across all sources so far. This one is in the 19th percentile – i.e., 19% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,693 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 23rd percentile – i.e., 23% of its peers scored the same or lower than it.
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We're also able to compare this research output to 211 others from the same source and published within six weeks on either side of this one. This one is in the 23rd percentile – i.e., 23% of its contemporaries scored the same or lower than it.