Bioinformatics analysis and cloning of fasciclin gene family in kiwifruit

Abstract:【Objective】Actinidia chinensis var. chinensis and A. chinensis var. deliciosa are mostly valu- able in the production of kiwifruit. Former research showed that male plants used as rootstocks had strong grafting advantages. Most of the rootstocks currently used in the production are 1-2 year old seedlings. Both female and male plants are used as rootstocks due to the lack of efficient method to distinguish the gender of the young seedlings, leading to the inconsistent growth and fruit quality of kiwi- fruit Therefore, it is very important to identify the gender of kiwifruit at the seedling stage. It was reported that the fasciclin genes were associated with the gender and participated in plant growth and pollen fertility development. The work was designed to study the biological information of fasciclin gene family in A. chinensis var. chinensis to provide theoretical basis for exploring the role of fasciclin genes in the differentiation of the male and female plants of kiwifruit and developing markers for identifying the male and female plants at seedlings stage.【Methods】The gene structure characteristics, evolutionary relationships, protein characteristics, promoter prediction, secondary structure of 38 fasciclin genes from the female plant of A. chinensis var. chinensis were analyzed by bioinformatics software A gender-relat- ed fasciclin gene, named FrBy, was cloned from the male and female plants of A. chinensis var. chinen- sis and A. chinensis var. deliciosa, respectively. and the FrBy gene sequence was analyzed using existing knowledge and affordable tools, including reference genome of the female plant named Red 5 ofA. chinensis var. chinensis.【Results】The 38 fasciclin genes were distributed on the remaining 18 chro- mosomes except for 1, 4, 5, 6, 7, 10, 11, 15, 16, 19 and 21 chromosomes. The genes encoded 133-606 amino acids in length,and the number of serine phosphorylation sites, threonine phosphorylation sites and tyrosine phosphorylation sites ranged from 10 to 56 3 to 26 and 0 to 8, respectively.The majority of serine phosphorylation sites were found in PSS24547.1 protein, the fasciclin protein on chromosome 8. A total of 110 transcription factors (TFs) were predicted in the 2 000 bp promoter region. The first threeTFs were BBR-BPC, TALE and AP2. They were all related to the sex development of plants. The binding sites of the TFs were not predicted from nine fasciclin genes, in which gene silencing might occur during evolution. The maximum motif structures were 9 and the minimum was 1 of the 38 fasciclingenes. The PSS11741.1, PS01642.1 and PSS24547.1 proteins were choosenas the most representive characteristic sequences to set up the homologous tertiary structure model. The tertiary structure analy- sis showed that the PSS016442.1 mostly contained the α-helices. The PSS24547.1 mostly contained theβ-folds and random curls The PSS11741.1 least contained the β-folds and random curls.About 68.42 percent of 38 fasciclin proteins were hydrophobic proteinw which were unstable. The 38 fasciclin proteins were clearly divided into two subgroups by UPGMA (unweighted pair-group method with arithmetic means) method, among them, the PSS24547.1 was in its own class. The FrBy gene with 723 bp se- quence that cloned from the male plant possessed a Fas conserved domain, the 723 bp sequence was on- ly aligned with a region on chromosome 8 of the reference genome of Red 5 (E-value is 5E-167).【Conclusion】The study showed that the fasciclin genes were not conservitive in the female plant of A. chinensis var. chinensis while the FrBy gene cloned from the male plant of A. chinensis var. chinensis was very conservitive. The 723 bp sequence was significantly related to the gender character of A. chinensisvar. chinensis. However the 723 bp sequence could not distinguish the gender of Actinidia chinensis var.deliciosa, as a functional dioecious plant. The differentiation of varietas might occrue earlier than that of gender in A. chinensis.