| In tropical coral islands of China,the vegetation and ecosystem are very fragile,where there is long sunshine time,high temperature,abundant rainfall throughout the year,and soils rich in calcium and phosphorus with high salinity and strong alkalinity-the p H ranges from 8.0 to 9.5.It is of great significance for the sustainable development of tropical coral islands to strengthen the related work about protection,restoration and scientific research of their vegetation ecosystems.Cordia subcordata,tree or shrub with gorgeous flowers,belongs to a special group in plant habits of Boraginaceae;it has the advantages of high temperature resistance,strong light resistance,drought resistance,barren resistance,and strong wind resistance;it is suitable for landscaping,beneficial to the vegetation restoration of tropical coral island,and has strong research and application value.In this study,chromosome number of C.subcordata was determined by chromosome preparation technology and karyotype analysis,which provided a reference for genome assembly at the chromosomal level;the whole genome and transcriptome of C.subcordata were determined by Illumina and Nanopore sequencing platforms,and the whole genome was assembled,annotated and comparative genomic studies were conducted at the same time.It is a deep understanding of the genetic background of C.subcordata will help to explore its adaptation mechanism to its habitats with high temperature,high salinity and strong alkalinity on tropical coral islands,and also lay a foundation for germplasm conservation and genetic breeding.The results are as follows:1.On karyotype analysis,the best sampling time of C.subcordata tips was 9:00?10:00 am and 14:00?14:30 pm;the optimal pretreatment was immersing the root tips in saturated p-dichlorobenzene for two hours.The number of chromosomes is 32,16pairs;the plants are diploid;the karyotype belongs to "1A" type,and the karyotype formula was 2n=2x=32=32m.All of them are middle centromeric chromosomes(m),and no companion bodies are found.2.A total of 125.0 Gb raw data was obtained by the second generation sequencing(NGS)technology,and 119.0 Gb Clean data was obtained after quality control for K-mer analysis.The genome size based on NGS was estimated at 524.3Mb using 17-mer.The total sequence number of the third generation sequencing(TGS)was 91.3 Gb.Genome was then assembled by TGS sequences and adjusted by Illumina short sequences.The assemble genome was 475.3 Mb with contig number of92 and contig N50 of 16.4 Mb.Using Hi-C sequencing data to extend contigs and construct scaffold,470.35 Mb of sequence length was observed and the contigs were anchored to 16 chromosomes to obtain chromosome-level genome of C.subcordata.3.26,615 genes were predicted in total,and each gene contained an average of5.38 exons,with an average exon length of 235.66 bp and an average intron length of640.28 bp.25,730 genes were functionally annotated,including 21,703 genes from Swissprot database,9,981 genes from KEGG database,14,029 genes from KOG database,16,046 genes from GO database,and 25,549 from NR database.Tandem repeats account for 57.94% of the genome.The number of r RNA,s RNA,regulatory and t RNA was 282,1,800,13 and 928,respectively.4.A total of 30,853 gene families of 18 species were identified by homologous clustering analysis of 17 species and C.subcordata,and 5394 gene families containing gene copies in all plants were identified.There are a total of 13,881 gene families in C.subcordata,including 8,101 single-copy gene families,5,780 multi-copy gene families,and 217 unique gene families.C.subcordata and Coffea eugenioides formed a sister group that branched out 77 million years ago.Gen family expandion and contraction analysis revealed 1,983 expansion and 4,818 contraction families,respectively. |
PDF Full Text Request