Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

Abstract

Background: Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics analysis of TLP gene family in B. napus and other three important Brassicaceae crops. Results: Here, we identified a total of 29 TLP genes from B. napus genome, and they distributed on 16 chromosomes of B. napus. The evolutionary relationship showed that these genes could be divided into six groups from Group A to F. We found that the gene corresponding to Arabidopsis thaliana AT1G43640 was completely lost in B. rapa, B. oleracea and B. napus after whole genome triplication. The gene corresponding to AT1G25280 was retained in all the three species we analysed, belonging to 1:3:6 ratios. Our analyses suggested that there was a selective loss of some genes that might be redundant after genome duplication. This study proposed that the TLP genes in B. napus did not directly expansion compared with its diploid parents B. rapa, and B. oleracea. Instead, an indirect expansion of TLP gene family occurred in its two diploid parents. In addition, the study further utilized RNA-seq to detect the expression pattern of TLP genes between different tissues and two subgenomes. Conclusions: This study systematically conducted the comparative analyses of TLP gene family in B. napus, discussed the loss and expansion of genes after genome duplication. It provided rich gene resources for exploring the molecular mechanism of TLP gene family. Meanwhile, it provided guidance and reference for the research of other gene families in B. napus.

Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.

“…All of these gene pairs were identified as segmental repeats, indicating that the amplification of the MYB-CC gene family in B. napus may be independent of tandem duplication. The same duplication pattern was reported in other gene families during the evolution from diploid to allotetraploid ( Li et al, 2019a ; Li et al, 2019b ; Wang et al, 2020 ), and the gene families were mainly influenced by segmental duplication resulting from WGT and allopolyploidy ( Li et al, 2017 ). Specifically, plants retain many duplicate chromosome blocks in their genomes due to polyploidization events, resulting in segmental duplication ( Cannon et al, 2004 ).…”

Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus

“…Genome-wide studies identifying gene families in B. napus have reported the frequent expansion of gene families such as HSF, GST, CRF, TLP, and bHLH, to name a few [ 54 , 55 , 56 , 57 , 58 ]. The difference in the size of the Dof gene family from Arabidopsis to B. napus indicates the expansion of the B. napus Dof gene family.…”

Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

“…However, the number of BnaCOBLs was close to the sum of the number of BraCOBLs and BolCOBLs after allopolyploidization. Furthermore, BnaCOBLs are highly syntenic to [ 52 – 55 ] and conserved in gene clusters of BraCOBLs and BolCOBLs ( Fig 1 ). We propose that whole-genome triplication event contributed to the expansion of BnaCOBLs .…”