Genome-wide Identification and Bioinformatics Analysis of CesA/Csl Gene Family in Rice

doi:10.13304/j.nykjdb.2024.0333

Abstract

Abstract:

Rice cellulose synthase supergene family is composed of CesA （cellulose synthase） and Csl （cellulose synthase-like protein）. In order to understand the sequence characteristics and expression characteristics of the members of the family， and explore their functions， bioinformatics methods were used to identify OsCesA/Csl genes in the whole rice genome. Their physical and chemical properties， conserved motifs， gene structure， systematic evolution， cis-acting elements， chromosome mapping and collinearity were analyzed. Their expression in different tissues and different plant hormone treatments were analyzed based on transcriptome data. The results showed that a total of 22 members of OsCesA/Csl family were identified in rice genome， and the length of gene coding sequence （CDS） was 774~3 648 bp， protein molecular weight was 28.55~132.16 kD， isoelectric point was 6.09~9.62， and average hydrophilic coefficient was -0.339~0.750. The subcellular localization of 22 members was on cell membrane or Golgi apparatus. Phylogenetic evolution divided 22 members into 2 categories： OsCesA and OsCsl， each containing 11 members. The family members were distributed on 11 chromosomes except chromosome 11. There were 2 sets of tandem repeat genes in rice， and there was better collinearity between rice and maize. OsCesA/Csl members had different tissue expression patterns， and each member responded to jasmonic acid， abscisic acid， gibberellin and auxin treatment in different degrees. Above results laid a foundation for further exploring the specific function of OsCesA/Csl gene family in the growth and development of rice.

Key words: rice, cellulose synthases, genome-wide identification, bioinformatics

摘要：

水稻纤维素合成酶超基因家族由纤维素合成酶基因（cellulose synthase，CesA）和类纤维素合酶基因（cellulose synthase-like protein，Csl）组成，为了解水稻CesA/Csl家族成员序列特征及表达特性，探究其功能，利用生物信息学方法在水稻全基因组中鉴定OsCesA/Csl基因，并对其理化性质、保守基序、基因结构、系统进化、顺式作用元件、染色体定位和共线性等进行分析，利用转录组数据分析OsCesA/Csl的组织表达和不同植物激素处理下的表达。结果表明，在水稻基因组中共鉴定到22个OsCesA/Csl成员，基因编码序列（coding sequence，CDS）长度为774~3 648 bp，蛋白质分子量为28.55~132.16 kD，等电点为6.09~9.62，平均亲水系数为-0.339~0.750，亚细胞定位在细胞膜或高尔基体上。系统进化分为OsCesA和OsCsl，各包含11个成员，分布在除第11号以外的11条染色体上。水稻中存在2组串联重复基因，与玉米更具共线性关系。不同OsCesA/Csl成员的组织表达模式不同，均不同程度地响应茉莉酸、脱落酸、赤霉素和生长素处理。以上研究结果为进一步探索OsCesA/Csl基因家族在水稻生长发育中的功能奠定基础。

关键词: 水稻, 纤维素合成酶, 全基因组鉴定, 生物信息学

CLC Number:

S511

Rongju WU, Nenggang CHEN, Huan LI, Xiaoqing YAN, Zhanlie YANG, Jun LIU. Genome-wide Identification and Bioinformatics Analysis of CesA/Csl Gene Family in Rice[J]. Journal of Agricultural Science and Technology, 2025, 27(11): 83-92.

吴荣菊, 陈能刚, 李欢, 鄢小青, 杨占烈, 刘军. 水稻CesA/Csl基因家族的全基因组鉴定及生物信息学分析[J]. 中国农业科技导报, 2025, 27(11): 83-92.

Figures/Tables 8

References 24

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基因名称 Gene name	基因号 Gene ID	编码序列Coding sequence/bp	氨基酸数量 Number of amino acids/aa	分子量Molecular weight/kD	等电点 pI	亲水性系数 Grand average of hydropathicity	亚细胞定位 Subcellular localization
OsCesA1	Os05g0176100	3 231	1 076	121.27	6.68	-0.191	细胞膜 Cell membrane
OsCesA2	Os03g0808100	3 222	1 073	120.68	7.86	-0.214	细胞膜 Cell membrane
OsCesA3	Os07g0424400	3 282	1 093	123.50	6.74	-0.248	细胞膜 Cell membrane
OsCesA4	Os01g0750300	2 970	989	111.03	6.09	-0.112	细胞膜 Cell membrane
OsCesA5	Os03g0837100	3 279	1 092	123.40	6.66	-0.242	细胞膜 Cell membrane
OsCesA6	Os07g0252400	3 279	1 092	122.41	7.60	-0.211	细胞膜 Cell membrane
OsCesA7	Os10g0467800	3 192	1 063	119.79	8.25	-0.288	细胞膜 Cell membrane
OsCesA8	Os07g0208500	3 246	1 081	120.79	8.03	-0.217	细胞膜 Cell membrane
OsCesA9	Os09g0422500	3 168	1 055	118.70	6.42	-0.213	细胞膜 Cell membrane
OsCesA10	Os12g0477200	1 017	338	37.46	9.53	-0.339	高尔基体 Golgi apparatus
OsCesA11	Os06g0601600	1 575	524	57.80	9.62	-0.278	细胞膜 Cell membrane
OsCslD1	Os10g0578200	774	257	28.55	9.10	0.750	高尔基体 Golgi apparatus
OsCslD2	Os06g0111800	3 513	1 170	130.14	7.49	-0.233	高尔基体 Golgi apparatus
OsCslD3	Os08g0345500	3 441	1 146	127.15	6.48	-0.227	高尔基体 Golgi apparatus
OsCslD4	Os12g0555600	3 648	1 215	132.16	8.13	-0.115	高尔基体 Golgi apparatus
OsCslD5	Os06g0336500	3 039	1 012	112.40	8.07	-0.144	高尔基体 Golgi apparatus
OsCslE1	Os09g0478100	2 214	737	83.50	8.38	-0.005	高尔基体 Golgi apparatus
OsCslE2	Os02g0725300	2 238	745	83.65	7.69	0.042	高尔基体 Golgi apparatus
OsCslE3	Os09g0478300	1 884	627	71.29	8.46	-0.189	高尔基体 Golgi apparatus
OsCslH1	Os10g0341700	2 253	750	83.83	6.93	0.062	高尔基体 Golgi apparatus
OsCslH2	Os04g0429500	1 500	499	55.21	6.60	0.183	高尔基体 Golgi apparatus
OsCslH3	Os04g0429600	2 379	792	88.49	8.43	-0.114	高尔基体 Golgi apparatus

基因名称 Gene name	基因号 Gene ID	编码序列Coding sequence/bp	氨基酸数量 Number of amino acids/aa	分子量Molecular weight/kD	等电点 pI	亲水性系数 Grand average of hydropathicity	亚细胞定位 Subcellular localization
OsCesA1	Os05g0176100	3 231	1 076	121.27	6.68	-0.191	细胞膜 Cell membrane
OsCesA2	Os03g0808100	3 222	1 073	120.68	7.86	-0.214	细胞膜 Cell membrane
OsCesA3	Os07g0424400	3 282	1 093	123.50	6.74	-0.248	细胞膜 Cell membrane
OsCesA4	Os01g0750300	2 970	989	111.03	6.09	-0.112	细胞膜 Cell membrane
OsCesA5	Os03g0837100	3 279	1 092	123.40	6.66	-0.242	细胞膜 Cell membrane
OsCesA6	Os07g0252400	3 279	1 092	122.41	7.60	-0.211	细胞膜 Cell membrane
OsCesA7	Os10g0467800	3 192	1 063	119.79	8.25	-0.288	细胞膜 Cell membrane
OsCesA8	Os07g0208500	3 246	1 081	120.79	8.03	-0.217	细胞膜 Cell membrane
OsCesA9	Os09g0422500	3 168	1 055	118.70	6.42	-0.213	细胞膜 Cell membrane
OsCesA10	Os12g0477200	1 017	338	37.46	9.53	-0.339	高尔基体 Golgi apparatus
OsCesA11	Os06g0601600	1 575	524	57.80	9.62	-0.278	细胞膜 Cell membrane
OsCslD1	Os10g0578200	774	257	28.55	9.10	0.750	高尔基体 Golgi apparatus
OsCslD2	Os06g0111800	3 513	1 170	130.14	7.49	-0.233	高尔基体 Golgi apparatus
OsCslD3	Os08g0345500	3 441	1 146	127.15	6.48	-0.227	高尔基体 Golgi apparatus
OsCslD4	Os12g0555600	3 648	1 215	132.16	8.13	-0.115	高尔基体 Golgi apparatus
OsCslD5	Os06g0336500	3 039	1 012	112.40	8.07	-0.144	高尔基体 Golgi apparatus
OsCslE1	Os09g0478100	2 214	737	83.50	8.38	-0.005	高尔基体 Golgi apparatus
OsCslE2	Os02g0725300	2 238	745	83.65	7.69	0.042	高尔基体 Golgi apparatus
OsCslE3	Os09g0478300	1 884	627	71.29	8.46	-0.189	高尔基体 Golgi apparatus
OsCslH1	Os10g0341700	2 253	750	83.83	6.93	0.062	高尔基体 Golgi apparatus
OsCslH2	Os04g0429500	1 500	499	55.21	6.60	0.183	高尔基体 Golgi apparatus
OsCslH3	Os04g0429600	2 379	792	88.49	8.43	-0.114	高尔基体 Golgi apparatus