Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus

Abstract

Late embryogenesis abundant (LEA) proteins are a diverse and large group of polypeptides that play important roles in desiccation and freezing tolerance in plants. The LEA family has been systematically characterized in some plants but not Brassica napus. In this study, 108 BnLEA genes were identified in the B. napus genome and classified into eight families based on their conserved domains. Protein sequence alignments revealed an abundance of alanine, lysine and glutamic acid residues in BnLEA proteins. The BnLEA gene structure has few introns (<3), and they are distributed unevenly across all 19 chromosomes in B. napus, occurring as gene clusters in chromosomes A9, C2, C4 and C5. More than two-thirds of the BnLEA genes are associated with segmental duplication. Synteny analysis revealed that most LEA genes are conserved, although gene losses or gains were also identified. These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family. Expression profiles analysis indicated that expression of most BnLEAs was increased in leaves and late stage seeds. This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family.

Rice Ribosomal Protein Large Subunit Genes and Their Spatio-temporal and Stress Regulation

“…Keyword search and homology-based identification through HMM are widely used practices in identifying genome-wide copies of the annotated genes (Kapoor et al, 2008; Liang et al, 2016). We then searched for genes starting with the prefix ‘L’ to select large subunit genes.…”

Genome-wide in silico analysis of dehydrins in Sorghum bicolor, Setaria italica and Zea mays and quantitative analysis of dehydrin gene expressions under abiotic stresses in Sorghum bicolor

“…Kn-type DHNs identified in Arabidopsis have not been observed in all the 3 crops (Close, 1996). It appears that LEA genes are highly conserved (Liang et al, 2016) among plants though gene losses or gains were noticed. Two regional duplication events were noticed in Setaria, while one segmental duplication event in Zea, mays.…”

“…DHNs/DHN-like proteins with ion (calcium in particular) binding activity might act either as calcium buffers or as calcium-dependent chaperones like calreticulin and calnexin (Alsheikh et al, 2003). Eight DHNs have been reported earlier in rice (Wang et al, 2007;Verma et al, 2017), 13 in barley (Tommasini et al, 2008), 10 in Arabidopsis (Hundertmark and Hincha, 2008), 11 in poplar (Liu et al, 2012), 9 in Malus (Liang et al, 2012, 4 in Vitis , and 23 in Brassica napus (Liang et al, 2016). However, the information regarding the number of diverse DHN-types in warm grasses like Setaria italica, Sorghum bicolor, and Zea mays is lacking.…”

Investigating the In Vitro Regeneration Potential of Commercial Cultivars of Brassica

“…To develop stress-resilient transgenic versions, it is necessary to determine the morphogenesis potential of these varieties. Although transformation of Brassica species has been reported in several studies [13][14][15][16][17][18][19][20][21][22], several Brassica genotypes remain recalcitrant to genetic transformation [2,19,23]. Several factors including susceptibility to Agrobacterium infection, choice of explant and tissue culture conditions mainly responsible for these variations have been identified [13,19,22].…”