COMPARATIVE GENOMIC IDENTIFICATION AND ANALYSES OF EPIDERMAL DIFFERENTIATION COMPLEX GENES IN TURTLES
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摘要:
发掘龟鳖表皮分化复合体(Epidermal Differentiation Complex, EDC)基因的序列特征和进化有助于解析其甲壳表皮特征的遗传基础和演化历史。文章对28个龟鳖的EDC基因进行了比较基因组学鉴定, 染色体定位、氨基酸含量、结构域、蛋白空间结构分析和演化历史的重塑。研究结果表明龟鳖EDC基因具有和其他爬行动物相同的四类基因家族, 其中简单表皮复合体(Simple epidermal differentiation complex, SEDC)基因家族成员通过多次串联重复事件, 实现基因扩张。龟鳖SEDC蛋白氨基酸组成高度多样化, SEDC和S100融合蛋白(S100-fused type proteins, SFTP)蛋白氨基酸含量存在类群(硬壳、软壳、棱皮)特异性, 这支持了龟鳖甲壳表皮结构的多样性。龟鳖S100钙结合蛋白A (S100 calcium binding protein A, S100A)和SFTP功能域和蛋白空间结构高度保守, 仅肽聚糖识别蛋白(Peptidolycan recognition protein3, PGLYRP3)的motif3存在鳖科特异性丢失。龟鳖特有的含有脯氨酸、半胱氨酸和缬氨酸的表皮分化蛋白(Epidermal Differentiation protein rich in Proline, Cysteine and Valine, EDPCV)来源于富含脯氨酸的表皮分化蛋白(Epidermal differentiation protein rich in proline 1, EDP1), 富含半胱氨酸和缬氨酸, 通过串联复制实现基因扩张。研究为进一步研究EDPCV在龟鳖中的作用提供了数据基础和理论依据。
Abstract:The epidermal differentiation complex (EDC) is a cluster of genes highly associated with keratinocytes differentiation and epidermal keratinization. This gene cluster plays an important role in the differentiation of epidermal tissues in amniotes, the formation of various skin appendages, and the keratinization process. Therefore, exploring the sequence characteristics and evolution of EDC genes in turtles can help elucidate the genetic basis and evolutionary history of their shell epidermis traits. Currently, there is a lack of systematic comparative analysis of the sequence characteristics and evolutionary levels of EDC genes across different turtle groups. This study performed comparative genomics identification of EDC in 28 turtles, including chromosomal localization, amino acid composition, domain analysis, protein spatial structure analysis, and the reconstruction of evolutionary history. The EDC genes in turtles exhibit the same four gene families found in other reptiles, with members of the SEDC gene family expanding through multiple tandem repeat events. The amino acid composition of turtle SEDC proteins is highly diverse, with SEDC and SFTP protein amino acid content showing group-specific characteristics (hard-shelled, soft-shelled, leatherback), which supports the diversity of shell epidermal structures in turtles. The functional domains and protein spatial structures of S100A and SFTP are highly conserved across turtle species, with motif 3 of PGLYRP3 showing a loss specific to the family Trionychidae. The turtle-specific EDPCV originates from EDP1, and mutations have enriched cysteine and valine, facilitating gene expansion through tandem duplication. This study provides a data foundation and theoretical basis for further research on the role of EDPCV in turtles.
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Keywords:
- EDC /
- Amino acid content /
- Gene expansion /
- EDPCV gene /
- Turtles
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图 1 龟鳖与其他爬行动物EDC基因的基因组分布
左图为龟鳖和其他爬行动物的物种树; 右图显示了表皮分化复合体(EDC) 基因的组成; 着色的矩形代表 EDC 基因的不同成员; 连接矩形的实线代表基因间的物理基因组连锁; 矩形中的数字表示基因数量
Figure 1. Genomic distribution of EDC genes in turtles and other reptiles
The left side illustrates a species tree of turtles and other reptiles, while the right side displays the distribution of the Epidermal Differentiation Complex (EDC) genes. Colored squares represent the identified EDC genes, and solid lines connecting the gene boxes indicate physical genomic linkage. The number in the rectangle indicates the gene numbers
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图 2 龟鳖EDC蛋白氨基酸组成
A. 龟鳖不同物种 EDC 蛋白的氨基酸组成; B. 龟鳖EDC基因氨基酸含量均值百分比趋势图; 蛋白展示顺序和图 1中EDC基因分布顺序一致; C. 鳖、龟SEDC示例(EDQM1和LOR)蛋白氨基酸序列, 重复序列用蓝色矩形标记; D. 不同龟鳖科间 CRNN 蛋白氨基酸组成的比较; 统计显著性为: 0.01<*P<0.05
Figure 2. Amino acid contents of turtle EDC proteins
A. The diagram shows the amino acid contents of EDC proteins across turtle species; B. The average distributions of amino acid content in turtles. The protein data are shown in the order of the corresponding genes in the EDC (Fig. 1); C. Amino acid sequences of exemplary SEDC proteins (EDQM1 and LOR) from softshell and hardshell turtles are shown, with sequence repeats highlighted in blue rectangles; D. The distribution of amino acid content of CRNN protein sequences across various turtle families; The level of significance: 0.01<*P<0.05
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图 3 龟鳖目SFTP的空间结构和PGLYRP3的motif分析
A. 鳖科和陆龟总科SFTP和S100A11蛋白的空间结构, 红色α螺旋标记为S100结构域; B. 矩形标记为 PGLYRP3蛋白motif区域
Figure 3. Spatial structure of SFTP and motif analysis of PGLYRP3 in turtles
A. The spatial structures of the SFTP and S100A11 proteins in the families of Trionychia and Testudinoidea, with the red α-helix labeled as the S100 domain; B. The rectangle marks the protein motif regions of the PGLYRP3
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图 4 龟鳖目SEDC基因系统发育分析及演化
A. 龟鳖SEDC基因系统发育树; 颜色标注不同家族成员; B. 龟鳖EDPCV基因起源及多样化模型
Figure 4. Phylogenetic analysis and the evolution of SEDC in turtles
A. Phylogenetic tree of SEDC genes in turtles; Colors indicate SEDC subfamilies; B. A scenario for the origin and diversification of EDPCV in turtles
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