Additional file 1 of Genome-wide identification, evolutionary and functional analyses of KFB family members in potato

Additional file 1 Table S1. The information of profile HMMs of F-box and Kelch domains in Pfam database. Table S2. The sequences and positions information of F-box domains in 44 StKFB members. Table S3. The sequences and positions information of Kelch motifs in 44 StKFB members. Table S4. The 20 conserved motifs in StKFB proteins identified by MEME software and motifs annotation analysis by InterProScan. Table S5. The orthologous KFB genes identified by comparison between potato and other plants. Table S6. Expression profiles of 44 StKFB genes in different potato tissues, in potato plants with different treatments and in tubers with different colors. The FPKM values of 44 StKFB genes in different potato tissues and in potato plants with different treatments were extracted from RNA-Seq Gene Expression Data: DM_RH_RNA-Seq_FPKM_expression_matrix_for_DM_v4.03_13dec2013_desc.xlsx, the excel file of FPKM values of all the representative transcripts across 40 DM and 16 RH libraries ( http://spuddb.uga.edu/pgsc_download.shtml ); the FPKM values in tubers with different colors was extracted from RNA-seq data in our lab deposited in the NCBI Sequence Read Archive under the Bioproject accession PRJNA729884. Table S7. Quality of transcriptome sequencing of potato tuber with three colors. Raw reads: Number of reads in raw data; Clean reads: Number of reads filtered from raw data; Raw bases: The number of bases in the raw data; Clean bases: The number of bases filtered from the raw data; Error rate: Error rate of data sequencing; Q20: Percentage of bases with a Phred value greater than 20; Q30: Percentage of bases with a Phred value greater than 30; GC content: The percentage of G and C in clean reads. Table S8. Sequence alignment results of reads mapped to the reference genome (DM v4.03/v4.04). Total reads: the number of clean reads used for mapping analysis; Total mapped: the number of reads that could be mapped to the reference genome; Multiple mapped: the number of reads mapped to multiple locations in the reference genome; Uniquely mapped: the number of reads mapped to single location in the reference genome; Read-1 and Read-2: the number of reads mapped to the reference genome in Read 1 and Read 2, respectively; Reads mapped to ‘+’ and Reads mapped to ‘-’: the number of reads mapped to the positive and negative strands of the reference genome, respectively; Non-splice reads: the number of reads with the entire segment mapped to exons; Splice reads: the number of segmented reads mapped on two different exons; Reads mapped in proper pairs:the number of reads paired mapped to the reference genome; Proper-paired reads map to different chrom: the number of paired reads mapped to different chromosomes in the reference genome. Table S9. All primers used in qRT-PCR. Table S10. The annotation of 44 StKFBs and their corresponding orthologous genes in Arabidopsis thaliana. The potato StKFB protein sequences were aligned with those of Arabidopsis thaliana using Blastp.

附加文件1 表S1：Pfam数据库中F-box结构域与Kelch结构域的轮廓隐马尔可夫模型（profile HMMs）信息。表S2：44个StKFB家族成员的F-box结构域序列及其位置信息。表S3：44个StKFB家族成员的Kelch基序序列及其位置信息。表S4：通过MEME软件鉴定的StKFB蛋白所含的20个保守基序，以及经InterProScan完成注释分析得到的基序注释结果。表S5：通过马铃薯与其他植物基因组比对鉴定得到的直系同源KFB基因。表S6：44个StKFB基因在马铃薯不同组织、不同处理条件下的植株以及不同颜色块茎中的表达谱。其中，44个StKFB基因在马铃薯不同组织与不同处理植株中的每百万片段转录本数（FPKM，Fragment Per Kilobase of transcript per Million mapped reads）值提取自RNA-seq基因表达数据文件DM_RH_RNA-Seq_FPKM_expression_matrix_for_DM_v4.03_13dec2013_desc.xlsx，该文件包含40个DM文库与16个RH文库中所有代表性转录本的FPKM值（数据来源网址：http://spuddb.uga.edu/pgsc_download.shtml）；不同颜色块茎中的FPKM值则提取自本实验室存档于NCBI序列读取归档（SRA）的RNA-seq数据，其生物项目登录号为PRJNA729884。表S7：三种颜色马铃薯块茎的转录组测序质量统计指标，具体包括：原始读段（Raw reads）：原始测序数据中的读段总数；清洁读段（Clean reads）：从原始数据中过滤得到的有效读段数量；原始碱基（Raw bases）：原始测序数据中的碱基总量；清洁碱基（Clean bases）：过滤后得到的有效碱基总量；错误率（Error rate）：测序数据的碱基识别错误率；Q20：Phred值大于20的碱基所占百分比；Q30：Phred值大于30的碱基所占百分比；GC含量（GC content）：清洁读段中鸟嘌呤（G）与胞嘧啶（C）碱基的占比。表S8：读段比对至参考基因组（DM v4.03/v4.04）的比对结果统计，具体指标包括：总读段数（Total reads）：用于比对分析的清洁读段总数；总比对读段数（Total mapped）：可比对至参考基因组的读段数量；多位置比对读段数（Multiple mapped）：比对至参考基因组多个不同位置的读段数量；唯一比对读段数（Uniquely mapped）：仅比对至参考基因组单个位置的读段数量；Read-1与Read-2：分别比对至Read 1与Read 2文库的读段数量；Reads mapped to ‘+’与Reads mapped to ‘-’：分别比对至参考基因组正链与负链的读段数量；非剪接读段（Non-splice reads）：全部片段均比对至单个外显子区域的读段数量；剪接读段（Splice reads）：分段跨越两个不同外显子区域的读段数量；正确配对比对读段数（Reads mapped in proper pairs）：配对两端均比对至参考基因组的读段数量；跨染色体配对比对读段数（Proper-paired reads map to different chrom）：配对读段分别比对至参考基因组不同染色体的读段数量。表S9：实时荧光定量PCR（qRT-PCR）所用的全部引物序列。表S10：44个StKFB基因的注释信息，以及它们在拟南芥（Arabidopsis thaliana）中对应的直系同源基因。本研究通过Blastp工具将马铃薯StKFB蛋白序列与拟南芥蛋白序列进行了同源比对。