| The development of cotton fiber cell mainly includes the synthesis of primary wall and the thickening of secondary wall.The content of pectin has an important effect on fiber quality.Alpha-galacturonosyltransferase(GAUT)and UDP-D-glucuronate 4-epimerase(GAE)are the key enzymes in the metabolism of pectin.It has a great significance to study the function of pectin in the process of fiber development.In this study,the members of GAUT and GAE gene family were identified at the whole genome level,and the expression patterns of GAUT and GAE gene family were determined based on the data of fiber development transcriptome.The main results were as follows:1.Fourty-six Gh GAUT genes were identified from the Gossypium hirsutum genome,and named Gh GAUT01-46.Gh GAUT45 and Gh GAUT46 were located on the scafflods which were not assembled into chromosomes.Thirty-seven Gb GAUT genes were identified in the G.barbadense genome and named Gb GAUT01-37,Gb GAE37 was located on the scafflod which was not assembled into chromosome.(1)According to the distribution of genes on chromosomes,Gh GAUT family was distributed on 20 different chromosomes.There were five genes on chromosome At07 and five genes on chromosome Dt07.Gb GAUT family members of G.barbadense were distributed on 18 chromosomes and there were five genes in Dt07,the others had only 1-3 GAUT genes.The tandem of some genes might lead to the expansion of the gene family.According to the phylogeny,the GAUT family was divided into three subgroups: subgroup I,II and III contained 26,21 and 36 GAUT genes,respectively.Most of the genes in subgroup I contained ten exons,and subgroup II contained nine exons,and three exons were the majority in subgroup III.(2)The peptide chain encoded by the Gh GAUT family of the G.hirsutum was composed of 563 amino acids on average,the molecular weight of which was mostly between 28.36~84.82 k D.The average peptide chain encoded by Gb GAUT was 570 amino acid,the molecular weight ranged from 43.29 to 107.77 k Da,and the average molecular weight was 65.48 k Da.The average molecular weight was slightly higher than that of G.hirsutum.The theoretical isoelectric point of Gh GAUT family was between 5.44~9.49,the average was 8.49.The Gb GAUT family’s theoretical isoelectric point was 5.46~9.51,and the average was 8.34,the average theoretical isoelectric point was slightly smaller than that of G.hirsutum.Most GAUT members were unstable proteins,and all of the GAUT family members had high liposolubility and were hydrophilic proteins.(3)There were many conserved domain in the GAUT family.Part of conserved amino acid residues comprised specific conserved motif of GAUT family.There were four common conserved motifs,but they also had differences in the distribution of these amino acids,which may lead to the differentiation of gene function.Subcellular localization prediction showed that all the Gh GAUTs and Gh GAUT were localized in the Golgi membrane,except for Gh GAUT45 and Gh GAUT46.The protein transmembrane domain analysis showed that about 85 % Gh GAUT and 68 % Gb GAUT had one transmembrane domains.(4)There were a variety of cis acting elements related to fiber development,light reaction,hormone regulation,biotic stress and abiotic stress in the upstream of GAUT family,which indicated the diversity function of GAUT gene family.(5)The gene expression of GAUT family was divided into four types by the data of cotton fiber transcriptome.There were high expression pattern of initial stage,high expression pattern of fiber elongation period,high expression pattern of secondary wall thickening period,and low expression pattern of the whole period.The difference of GAUT expression was analyzed between high quality upland cotton and general quality upland cotton,and between high quality island cotton and high quality upland cotton at the same time of fiber development.The results showed that Gb GAUT34 was preferentially expressed at the initial stage;Gh GAUT02,GGAUT12,Gh GAUT24,Gb GAUT10,Gb GAUT32 were preferentially expressed at fiber elongation period;Gb GAUT25,Gb GAUT17,Gb GAUT19 were preferentially expressed at the initial stage and the fiber elongation period,and Gb GAUT01,Gb GAUT05,Gb GAUT11 were preferentially expressed at the secondary wall thickening stage.These genes might be an important factor leading to longer fiber in the high quality cotton than that in the general quality cotton.2.21 and 22 GAEs family members were identified in the genome of G.hirsutum and G.barbadense,respectively,named Gh GAE01-21 and Gb GAE01-22.The Gh GAE02,Gh GAE14,Gb GAE11 and Gb GAE20 are located on large fragments.(1)According to the distribution on chromosomes,GAEs family members of G.hirsutum and G.barbadense were distributed on 12 chromosomes.There were four Gh GAE genes on At08 and Dt08 in G.hirsutum,respectively.In G.barbadense,there were four and six Gb GAE on A08 and D08,the other chromosomes had only 1-2 genes.According to phylogenetic analysis,we could divide the GAE family into three subgroups,I,II and III subgroups contained 17,8 and 18 genes,respectively.Genetic structure analysis showed that 72% of GAEs gene had no intron,which was similar to that of Arabidopsis GAE family.(2)The peptide chain encoded by the Gh GAE family in G.hirsutum was composed of 414 amino acids on average,and the molecular weight was between 24.87~50.32 k Da,with an average of 45.93 k Da.The average peptide chain encoded by Gb GAEs was 426 amino acids.The average molecular weight was 47.29 k Da.The average molecular weight was higher than that of G.hirsutum.The theoretical isoelectric point of Gh GAEs family was between 9.02~10.34,and the average is 9.79.Gb GAEs family with a theoretical isoelectric point of 9.01~9.98 and an average of 9.67.Most of them were unstable proteins,and all Gh GAEs and Gb GAEs had high liposolubility and were hydrophilic proteins(3)There were many conserved domain in the GAE family.Part of conserved amino acid residues comprised specific conserved motif of GAE family.There were four common conserved motifs,but they also had differences in the distribution of these amino acids,which may lead to the differentiation of gene function.Subcellular localization prediction showed that all of the Gh GAEs and Gb GAEs proteins were located in Golgi membrane.Protein transmembrane analysis showed that Gh GAE12,Gb GAE05,Gb GAE06,Gb GAE17,Gb GAE18 and Gb GAE22 had no transmembrane domain,the rest family members contained 1~2 transmembrane domains,while Gh GAE01,Gh GAE11 and Gb GAE11 contained 3 transmembrane regions.(4)There were many cis-acting elements related to fiber development,light response,hormone regulation,biotic stress and abiotic stress in the upstream of GAE family,indicating the diversity function of GAE family.(5)The gene expression of GAE family was divided into four types by the data of cotton fiber transcriptome.There were high expression pattern of initial stage,high expression pattern of fiber elongation period,high expression pattern of secondary wall thickening period,and low expression pattern of the whole period.The difference of GAE expression was analyzed between high quality upland cotton and general quality upland cotton,and between high quality island cotton and high quality upland cotton at the same time of fiber development.Gh GAE10,Gb GAE08,Gb GAE10 were preferentially expressed at fiber elongation stage;Gh GAE11,Gh GAE19 were preferentially expressed at secondary wall thickening stage;Gh GAE08,Gb GAE06 were preferentially expressed at fiber elongation and secondary wall thickening stage;Gb GAE07 was preferentially expressed at fiber initiation and secondary wall thickening stage.These genes might be an important factor leading to longer fiber in the high quality cotton than that in the general quality cotton.In summary,the essential information of GAUT,GAE gene family members in G.hirsutum and G.barbadense was explicited,and the expression of GAUT and GAE gene was analyzed at different time points of fiber development,and the candidated genes which played a key role in cotton fiber development were excavated.These results lay a solid foundation for studying the function of GAUT and GAE gene family in cotton fiber development. |
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