生物技术通报 ›› 2022, Vol. 38 ›› Issue (9): 180-190.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0344
收稿日期:
2022-03-22
出版日期:
2022-09-26
发布日期:
2022-10-11
作者简介:
司诚,女,硕士研究生,研究方向:作物遗传与生长发育;E-mail: 基金资助:
SI Cheng1,2(), ZHONG Qi-wen1, YANG Shi-peng1()
Received:
2022-03-22
Published:
2022-09-26
Online:
2022-10-11
摘要:
香瓜茄又名人参果,具有抗氧化、抗肿瘤、抗糖尿病等多种生物活性。为丰富茄科作物基因组信息及进化发育历程,获取香瓜茄全基因组序列信息,同时为香瓜茄相关分子研究奠定基础。以香瓜茄植物组织为试验材料,基于Illumina HiSeq构建小片段文库进行基因组特征评估,利用PacBio三代测序技术、Hi-C技术构建及组装香瓜茄全基因组数据库。利用生物信息学方法对获得的基因组序列进行组装、功能注释以及进化分析研究。结果表明,获得54.11 Gb Illumina HiSeq数据;获得55.08 Gb PacBio数据,reads平均长度为14 179 bp;获得Hi-C数据量约143 Gb;拼接得到该基因组contig序列总长为1.16 Gb,Hi-C纠错后contig N50为22.63 Mb;Hi-C挂载染色体,共有1.12 Gb长度的序列可以挂载到12条染色体上,占比97.16%;其中,能够确定顺序和方向的序列长度为1.08 Gb,占定位染色体序列总长度的96.11%,得到基因组大小1.25 Gb;预测有64.22%的重复序列,41 571个基因,99.06%的基因可以注释到NR、GO、KEGG等数据库中;预测得到4 360个tRNA、5 677个rRNA、154个miRNA;得到449个假基因。香瓜茄与马铃薯的进化时间大约在12.82 MYA。
司诚, 钟启文, 杨世鹏. 基于PacBio三代测序的香瓜茄(人参果)基因组的组装[J]. 生物技术通报, 2022, 38(9): 180-190.
SI Cheng, ZHONG Qi-wen, YANG Shi-peng. Assembly of Pepino Genome Based on PacBio's Third-generation Sequencing Technology[J]. Biotechnology Bulletin, 2022, 38(9): 180-190.
K-mer | K-mer总数量Total K-mer number | K-mer深度K-mer depth | 基因组大小Genome size/Mb | 修正后基因组大小Corrected genome size/Mb | 杂合率Heterozygosity/% | 重复序列比例 Repeat sequence ratio/% |
---|---|---|---|---|---|---|
6 | 38 824 569 291 | 31 | 1 252.41 | 1 238.06 | 0.84 | 65.87 |
表1 香瓜茄基因组特征
Table 1 Pepino genomic characteristics
K-mer | K-mer总数量Total K-mer number | K-mer深度K-mer depth | 基因组大小Genome size/Mb | 修正后基因组大小Corrected genome size/Mb | 杂合率Heterozygosity/% | 重复序列比例 Repeat sequence ratio/% |
---|---|---|---|---|---|---|
6 | 38 824 569 291 | 31 | 1 252.41 | 1 238.06 | 0.84 | 65.87 |
项目Item | 总长度Total length/bp | 总数量Total number | 最大长度Max length/bp | N50长度N50-length/bp | N90长度N90-length/bp |
---|---|---|---|---|---|
Contig | 1 141 353 553 | 1 952 498 | 125 830 | 2 049 | 165 |
Scaffold | 1 169 596 440 | 1 679 956 | 191 961 | 3 185 | 199 |
表2 组装结果统计
Table 2 Statistics of assembly results
项目Item | 总长度Total length/bp | 总数量Total number | 最大长度Max length/bp | N50长度N50-length/bp | N90长度N90-length/bp |
---|---|---|---|---|---|
Contig | 1 141 353 553 | 1 952 498 | 125 830 | 2 049 | 165 |
Scaffold | 1 169 596 440 | 1 679 956 | 191 961 | 3 185 | 199 |
图2 Contig覆盖深度、长度和数量分布图 a:contig覆盖深度和长度分布图;b:contig覆盖深度和数量分布图
Fig. 2 Contig coverage depth, length and number distribution map a:Length distribution chart. b:Quantity distribution chart
重叠群数目 CtgNum | 重叠群长度 CtgLen/bp | 重叠群N50长度 CtgN50/bp | 重叠群N90长度 CtgN90/bp | 最长重叠群长度 CtgMax/bp | 碱基含量 GC/% |
---|---|---|---|---|---|
1 813 | 1 156 071 317 | 22 628 432 | 596 645 | 83 851 337 | 35.83 |
表3 组装结果的统计信息
Table 3 Statistical information of assembly results
重叠群数目 CtgNum | 重叠群长度 CtgLen/bp | 重叠群N50长度 CtgN50/bp | 重叠群N90长度 CtgN90/bp | 最长重叠群长度 CtgMax/bp | 碱基含量 GC/% |
---|---|---|---|---|---|
1 813 | 1 156 071 317 | 22 628 432 | 596 645 | 83 851 337 | 35.83 |
项目Item | 基因组信息Genome information |
---|---|
总数TotalNum | 1 566 |
最小长度MinLen | 1 000 |
Scaffold的数量ScfNum | 1 566 |
Scaffold的长度ScfLen/bp | 1 156 096 017 |
Scaffold N50长度ScfN50/bp | 87 253 278 |
Scaffold N90长度ScfN90/bp | 74 267 810 |
最长的scaffold ScfMax/bp | 111 830 586 |
Scaffold数目mScfNum | 0 |
Scaffold的长度mScfLen | 0 |
Contig数目CtgNum | 1 813 |
Ctg长度CtgLen/bp | 1 156 071 317 |
Contig N50的长度CtgN50/bp | 22 628 432 |
Contig N90的长度CtgN90/bp | 596 645 |
最长的contig CtgMax/bp | 83 851 337 |
GC含量GC/% | 35.83 |
Contig数目GapNum | 247 |
Gap长度GapLen/bp | 24 700 |
最大的gap MaxGap | 100 |
表4 香瓜茄Hi-C组装的基因组信息
Table 4 Hi-C assembly information of the pepino genome
项目Item | 基因组信息Genome information |
---|---|
总数TotalNum | 1 566 |
最小长度MinLen | 1 000 |
Scaffold的数量ScfNum | 1 566 |
Scaffold的长度ScfLen/bp | 1 156 096 017 |
Scaffold N50长度ScfN50/bp | 87 253 278 |
Scaffold N90长度ScfN90/bp | 74 267 810 |
最长的scaffold ScfMax/bp | 111 830 586 |
Scaffold数目mScfNum | 0 |
Scaffold的长度mScfLen | 0 |
Contig数目CtgNum | 1 813 |
Ctg长度CtgLen/bp | 1 156 071 317 |
Contig N50的长度CtgN50/bp | 22 628 432 |
Contig N90的长度CtgN90/bp | 596 645 |
最长的contig CtgMax/bp | 83 851 337 |
GC含量GC/% | 35.83 |
Contig数目GapNum | 247 |
Gap长度GapLen/bp | 24 700 |
最大的gap MaxGap | 100 |
图5 香瓜茄基因组Hi-C组装染色体交互热图 横坐标、纵坐标均代表每个bin在相应染色体群组上的Order
Fig. 5 Hi-C assembly chromosome interaction heat map of pepino genome Both horizontal and vertical coordinates represent the Order of each bin on the corresponding chromosome group
方法 Method | 软件 Software | 物种 Species | 基因数目 Gene number |
---|---|---|---|
Ab initio | Augustus | 26 025 | |
SNAP | 47 891 | ||
Homology-based | GeMoMa | 拟南芥A. thaliana | 26 652 |
辣椒C. annuum | 37 150 | ||
番茄S. lycopersicum | 32 312 | ||
潘那利番茄 S. pennellii | 33 755 | ||
马铃薯S. tuberosum | 51 586 | ||
RNAseq | GeneMarkS-T | 19 020 | |
PASA | 12 454 | ||
Integration | EVM | 41 571 |
表5 香瓜茄基因预测结果
Table 5 Prediction results of pepino gene
方法 Method | 软件 Software | 物种 Species | 基因数目 Gene number |
---|---|---|---|
Ab initio | Augustus | 26 025 | |
SNAP | 47 891 | ||
Homology-based | GeMoMa | 拟南芥A. thaliana | 26 652 |
辣椒C. annuum | 37 150 | ||
番茄S. lycopersicum | 32 312 | ||
潘那利番茄 S. pennellii | 33 755 | ||
马铃薯S. tuberosum | 51 586 | ||
RNAseq | GeneMarkS-T | 19 020 | |
PASA | 12 454 | ||
Integration | EVM | 41 571 |
功能注释数据库Function-annotated database | 注释到的基因数目Number of annotated genes | 占总数据库的百分比Percentage in database /% |
---|---|---|
GO_Annotation | 30 713 | 73.88 |
KEGG_Annotation | 29 114 | 70.03 |
KOG_Annotation | 20 636 | 49.64 |
Pfam_Annotation | 31 802 | 76.5 |
Swissprot_Annotation | 28 876 | 69.46 |
TrEMBL_Annotation | 41 085 | 98.83 |
eggNOG_Annotation | 32 433 | 78.02 |
nr_Annotation | 40 785 | 98.11 |
All_Annotated | 41 179 | 99.06 |
表6 香瓜茄基因功能注释统计信息
Table 6 Statistical information of pepino gene function annotation
功能注释数据库Function-annotated database | 注释到的基因数目Number of annotated genes | 占总数据库的百分比Percentage in database /% |
---|---|---|
GO_Annotation | 30 713 | 73.88 |
KEGG_Annotation | 29 114 | 70.03 |
KOG_Annotation | 20 636 | 49.64 |
Pfam_Annotation | 31 802 | 76.5 |
Swissprot_Annotation | 28 876 | 69.46 |
TrEMBL_Annotation | 41 085 | 98.83 |
eggNOG_Annotation | 32 433 | 78.02 |
nr_Annotation | 40 785 | 98.11 |
All_Annotated | 41 179 | 99.06 |
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