| Moso bamboo(Phyllostachys edulis)is the most important economic bamboo species in China,which has a huge economic,ecological and social benefits.Phyllostachys edulis ‘Pachyloen' is a elite germplasm with thick wall,optimal shoots,strong resistance and genetic stability in moso bamboo variations.It has important value in production and scientific research.Phyllostachys edulis ‘Pachyloen' germplasm characters have a systematic general biology research results.This is the first time to study the Phyllostachys edulis ‘Pachyloen' as resequencing material from the whole genome level,studying its important molecular mechanism of germplasm traits.At the same time,we used Phyllostachys nidularia f.farcta,Phyllostachys heteroclada f.decurtata with thick wall germplasm traits and Schizostachyum dumetorum var.xinwuense with thin-walled germplasm traits to carry out the whole genome sequencing.The genes of thick wall were researched using gene set reduction method.The main results were shown below:(1)This rsearch got 24.50 Gb raw data with the 12× depth coverage of genome of Phyllostachys edulis ‘Pachyloen'.The reads number was 245 245 627 comparing with the reference genome of moso bamboo,and its matching rate was 97.43%.We got 33.01 Gb raw data of Phyllostachys nidularia f.farcta,the reads number was 89 627 635 comparing with the reference genome of moso bamboo,and its matching rate was 37.93%.We got 28.29 Gb raw data of Phyllostachys heteroclada f.decurtata,the reads number was 78 878 955 comparing with the reference genome of moso bamboo,and its matching rate was 38.97%.We got 34.55 Gb raw data of Schizostachyum dumetorum var.xinwuense,the reads number was 8 009 527 comparing with the reference genome of moso bamboo,and its matching rate was 1.44%.(2)There were 1 718 960 SNPs in Phyllostachys edulis ‘Pachyloen',and a mutation occurred per 1 093 bases averagely with an Transition/Transversion ratio(Ts/Tv)of 2.93.Phyllostachys nidularia f.farcta were found to have 19 727 178 SNPs,and there is a mutation around in 94 bases,with an Ts/Tv of 3.05.There are 18 041 778 SNPs in Phyllostachys heteroclada f.decurtata,on average,there was mutation in 103 bases,with an Ts/Tv of 3.00.1 683 311 SNPs are identified in Schizostachyum dumetorum var.xinwuense,and there was a mutation around in 958 bases,with an Ts/Tv of 1.54.The ratio of SNPs occurred in exon region is different in four bamboos,from large to small in turn was Schizostachyum dumetorum var.xinwuense,Phyllostachys heteroclada f.decurtata,Phyllostachys edulis ‘Pachyloen',Phyllostachys nidularia f.farcta,the proportions were 37.97%,2.56%,2.53% and 2.25%,respectively..(3)In Del: The number of In Dels in Phyllostachys edulis ‘Pachyloen' was 72 337,including 380 40 insertions,34 297 deletions.The number of In Dels in Phyllostachys nidularia f.farct was 489 064,including 229 721 insertions and 259 745 deletions.The number of In Dels in Phyllostachys heteroclada f.decurtata was 335 745,including 159 491 insertions and 176 254 deletions.The number of In Dels in Schizostachyum dumetorum var.xinwuense was 31 939,including 14 778 insertions and 17 161 deletions.The percentage of In Dels in exons from large to small in turn were Schizostachyum dumetorum var.xinwuense,Phyllostachys heteroclada f.decurtata,Phyllostachys edulis ‘Pachyloen',Phyllostachys nidularia f.farct,the proportions were 18.42%,3.66%,3.41% and 2.91%,respectively.Most of the In Dels was 1 bp short sequence in the genome sequence,leading to frameshift mutations,and it became the important impetus of genome evolution.(4)A total number of 558 437 CNVs were identified in Phyllostachys edulis ‘Pachyloen',including 158 185 duplications and 400 252 deletions respectively.These CNVs uneven distribution in 5 269 genes.In the vast majority of genes that appeared on CNVs number was less than 10,only 20 genes which had the CNVs number more than 10.The gene PH01000028G2090 which had 124 CNVs,expressing protein as the gene function.(5)GO enrichment: 6 631 diffrential genes were found in Phyllostachys edulis ‘Pachyloen',4 243 genes related with biological process were enriched,1 798 genes related with cellular component were enriched,6 111 genes related with molecular functiom were enriched.17 328 diffrential genes were found in Phyllostachys nidularia f.farct,105 384 genes related with biological process were enriched,4 730 genes related with cellular component were gathered,15 837 genes related with molecular functiom were enriched.13 896 diffrential genes were found in Phyllostachys nidularia f.farct,8 718 genes related with biological process were enriched,3 959 genes related with cellular component were enriched,12 737 genes related with molecular functiom were enriched.The quantity of genes was very different among different bamboo species and GO terms,this may be related with the conservative level of the fountions of genes.(6)KEGG Pathway:There were 1 210 differential genes involved in 116 metabolic pathways in Phyllostachys edulis ‘Pachyloen',compared with 3 470 differential genes involved in 119 metabolic pathways in Phyllostachys nidularia f.farct,3 474 differential genes involved in 119 metabolic pathways in Phyllostachys heteroclada f.decurtata,3 045 differential genes involved in 118 metabolic pathways in Schizostachyum dumetorum var.xinwuense.12 metabolic pathways were studied,it showed that 151 genes changed,such as PH01000648G0610 etc.These genes were related with the compound and transpotion of starch,sugar,hormones,and basic cell materials in the ribosome and the sendoplasmic reticulum,which involved sugar,protein and lipid.(7)After comparative genomics research of bamboos with thick culm wall and thin culm wall,we found 3 165 genes were related with thick culm wall,2 411 genes were related with biological process,1 180 genes were related with cellular component,2 943 genes were related with molecular function.It showed that 633 genes can matched on known metabolic pathways.Part of the metabolic process of energy,elements and amino acids were studied,and a group of amino acid codons chnging which were because of SNP or In Del.Its direct or significant relationship with quality characters of Phyllostachys edulis ‘Pachyloen' need further study. |
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