Genome-wide identification of SAUR genes in watermelon (Citrullus lanatus)

Abstract

The early auxin responsive SAUR family is an important gene family in auxin signal transduction. We here present the first report of a genome-wide identification of SAUR genes in watermelon genome. We successfully identified 65 and provide a genomic framework for future study on these genes. Phylogenetic result revealed a Cucurbitaceae-specific SAUR subfamily and contribute to understanding of the evolutionary pattern of SAUR genes in plants. Quantitative RT-PCR analysis demonstrates the existed expression of 11 randomly selected SAUR genes in watermelon tissues. was highly expressed in fruit, for which further study might bring a new prospective for watermelon fruit development. Moreover, correlation analysis revealed the similar expression profiles of SAUR genes between watermelon and Arabidopsis during shoot organogenesis. This work gives us a new support for the conserved auxin machinery in plants.

Genome-Wide Analysis of Watermelon HSP20s and Their Expression Profiles and Subcellular Locations under Stresses

“…In this study, we identified 44 ClHSP20s in watermelon, fewer than in switchgrass (63), soybean (51), and cucumber (45), but more than in the other species (Table 1). Although the genome size of watermelon (425 Mb) is obviously bigger than in Arabidopsis (125 Mb) and cucumber (367 Mb), the sizes of many gene families in watermelon are similar to those in cucumber but slightly smaller than those in Arabidopsis [36,37,38]. This is probably because watermelon avoided more recent wholegenome duplication events, except for the core-eudicot common hexaploidization (ECH) event [39,40].…”

“…However, the number of HSP20s in watermelon is twice than that in Arabidopsis in this study, which appears to contradict the above findings [39], but is consistent with the latest research that a cucurbit-common tetraploidization (CCT, 90–102 Mya) event occurred in the Cucurbitaceae shortly after the ECH event (115–130 Mya) [33]. The 13 tandemly duplicated gene pairs of ClHSP20s arose 6.65 to 135.02 Mya, probably as a result of gene losses and chromosomal rearrangements after the CCT event, However, there are relatively low rates of preserved CCT colinear genes in the watermelon genome (2.5–5.5%), which explains why many other watermelon gene families are quite small [36,37,38,39]. Watermelon has retained high genomic homology and it shares more colinear genes with cucumber [33].…”

Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response

“…The first SAUR gene was identified from elongating hypocotyls of auxin-treated soybean ( Glycine max ) [ 9 ]. Over the past 30 years, members of the SAUR gene family have been identified in many other species of angiosperms and thus comprise a large gene family in plants, such as Arabidopsis thaliana (81 SAUR genes, including two pseudogenes) [ 2 ], Oryza sativa (58 including two pseudogenes) [ 10 ], Zea mays (79) [ 3 ], Gossypium raimondii (145) [ 11 ], Citrus sinensis (70) [ 12 ], Phyllostachys edulis (44) [ 13 ], Boehmeria nivea (71) [ 14 ] and Citrullus lanatus (65) [ 15 ]. Many members of the SAUR gene family are a result of a high frequency of tandem and segmental duplications, and which have contributed to functional redundancy among the paralogues [ 6 ].…”

Identification and Expression of SAUR Genes in the CAM Plant Agave

“…Recently, the rapid development of next-generation sequencing (NGS) allows researchers to obtain and explore more information [21]. For example, genome-wide identification of SAUR genes has been performed in rice [22], Arabidopsis , maize, sorghum [23], tomato, potato [24], citrus [17], moso bamboo [25], watermelon [26], cotton [27] and poplar [28]. Moreover, most of those contain the species-specific expansion pattern, which probably contributes to the evolution of special traits among different species [23,26].…”

“…For example, genome-wide identification of SAUR genes has been performed in rice [22], Arabidopsis , maize, sorghum [23], tomato, potato [24], citrus [17], moso bamboo [25], watermelon [26], cotton [27] and poplar [28]. Moreover, most of those contain the species-specific expansion pattern, which probably contributes to the evolution of special traits among different species [23,26]. Consider SAUR genes are crucial effectors of hormonal and environmental signals, functional characterization of SAUR genes will broaden our understanding in plant growth and development [29,30].…”