Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome

Abstract

GRAS genes belong to the plant-specific transcription factors (TF's) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF's. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein-protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops. Transcription factors (TFs) are the class of proteins that control the functioning of various genes by binding with their promoters and thus involved in the gene regulation process 1. Previously, more than 320K TFs belonging to 58 transcription factor families have been reported from 165 different plant species. Out of these, GRAS represents one of the major families that are involved in plant growth, development, cell signaling, and stress tolerance 2. GRAS family was first reported in bacteria and characterized by the three TFs i.e. (i) GAI (gibberellicacid insensitive); (ii) RGA (repressor of GAI), and (iii) SCR (scarecrow) with the size range from 400 to 770 amino acids 3,4. It was observed that GAI and RGA are the part of DELLA proteins that take part in gibberellin (GA) and Jasmonate (JA) response as well as light signaling. Likewise, SCR and Short Root (SHR) played a key role in the radial organization of root by forming the SCR/SHR complex 5. Previously, it has also been reported that the C-terminal region of GRAS members is highly conserved, while the N-terminal is highly divergent that might provide the specificity to each protein 6. Furthermore, the evolutionary analysis suggested the phenomenon of horizontal gene transfer (HGT) from bacteria to plants. GRAS gene family is further categorized into different subfamilies such as eight in Arabidopsis and rice 7 , while 8 to 13 in tomato, popular, castor beans, etc 8-10. Recently, Cenci et al. classified the GRAS family into 17 subfamilies such as DELLA, Lateral suppressor (LS), Hairy meristem (HAM), and SCR 11. Previous studies showed that it is one of the widely explored transcription factor family in the various plant species including tomato, potato, buckwheat, and sweet orange 12-14. Bottle gourd (Lagenaria siceraria), a member of the Cucurbitaceae family is commonly cultivated in the tropical and subtropical regions an...

Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

“…The GRAS gene family has been extensively studied in many plant species: once the GRAS genes of the model organisms Arabidopsis and rice were identified [ 6 – 8 ], these genes could be more widely explored in many other species. This family has been identified and analyzed at the whole-genome level in Solanum lycopersicum [ 43 ], Vitis vinifera [ 44 ], castor bean [ 45 ], Malus domestica [ 46 ], Zea mays [ 47 ], Camellia sinensis [ 48 ], Gossypium hirsutum [ 49 ], Capsicum annuum [ 50 ], Dendrobium catenatum [ 51 ], Juglans regia [ 52 ], Fagopyrum tataricum [ 53 ], Brassica napu s [ 54 ], Citrus sinensis [ 55 ], Hordeum vulgare [ 56 ], Manihot esculenta [ 57 ], Lagenaria siceraria [ 58 ] and others. However, knowledge of the GRAS gene family in S. bicolor is still very limited.…”

Multifarious Roles of GRAS Transcription Factors in Plants

“…It has been reported that these motifs interact with the GA-bound receptor GA-2017), walnut (Quan et al, 2019) and clover (Zhang et al, 2017). However, in other plant species, the number of subfamilies is higher, for instance, 13 subfamilies were identified in the case of Populus trichocarpa (Liu and Widmer, 2014), Camellia sinensis (Wang et al, 2018) and castor bean (Xu et al, 2016) and 16 subfamilies were identified in bottle gourd (Sidhu et al, 2020).…”

“…Eudicot 21 08 (Chen et al, 2015) Oryza sativa (rice) Poaceae Monocot (Tian et al, 2004) Panax ginseng (ginseng) Araliaceae Eudicot (Wang et al, 2020b) Physcomitrella patens (moss) Funariaceae Monocot 13 (Wu et al, 2014) Populus tremula (populus) et al, 2008), Amborella trichopoda (Albert et al, 2013), Capsicum annum , Coffea canephora (Denoeud et al, 2014), Fragaria vesca (Chen et al, 2019a), Gossypium hirsutum (Zhang et al, 2018), Lagenaria siceraria (Sidhu et al, 2020), Musa acuminate (D'Hont et al, 2012), Oryza sativa (Tian et al, 2004), Phoenix dactylifera (Al-Mssallem et al, 2013), Theobroma cacao (Argout et al, 2011) and Vitis vinifera (Grimplet et al, 2016). MEGA X aligned the GRAS protein sequences (581) of the 12 plant species with the MUSCLE method.…”

Genome-wide Characterization of GRAS Transcription Factors and Their Potential Roles in Development and Drought Resilience in Rose (Rosa chinensis)

“…The GRAS proteins of the four species were grouped into 17 different subfamilies. Out of 17, 16 subfamilies (PAT1, LISCL, SCL3, SCL32, DELLA, SCR, DLT, HAM, LAS, SCL4/7, SHR, SCLA, RAD1, RAM1, NSP1, NSP2) were designated according to previous studies (Cenci and Rouard, 2017;Sidhu et al, 2020;Tian et al, 2004). A remaining Rosaceae-speci c subfamily (contains only rose and strawberry GRAS proteins) which is not grouped into any of the earlier reported subfamilies was named as Rc2 subfamily.…”

“…In Arabidopsis and rice, the GRAS genes were grouped into eight subfamilies, including-(i) DELLA, (ii) Hairy meristem(HAM), (iii) Light signaling through interactions light-responsive transcription factor PIFs (LISCL), (iv) Lateral suppressor (LS or LAS), (v) Phytochrome A signal transduction1 (PAT1), (vi) Scarecrow-like3 SCL3, (vii) SCR, and (viii) short-root (SHR) (Lee et al, 2008;Tian et al, 2004). However, in other plant species, the number of subfamilies were reported higher than 8; for instance, 13 subfamilies were identi ed in the case of Populus trichocarpa (Liu and Widmer, 2014), Camellia sinensis (Wang et al, 2018) and castor bean (Xu et al, 2016), 14 subfamilies were identi ed in strawberry (Chen et al, 2019) and cotton (Zhang et al, 2018) and 16 subfamilies were identi ed in bottle gourd (Sidhu et al, 2020).…”