In 2021, BMKGENE witnessed 31 De novo genome research successfully published in high-impact journals with total impact factors over 320. 15 of the articles were co-authored 4 of them were co-authored as the first authors by BMKGENE
Right after the beginning of year 2022, there have been already two research articles published on journal “Natural Genetics” and “Molecular Plant” respectively. They are, “Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars” (Lychee genome research, conducted by College of Horticulture, South China Agricultural university, and scientific collaborators, published on Natural Genetics.), and “Genome sequences of the five Sitopsis species of Aegilops and the origin of polyploid wheat B-subgenome” (Five Sitopsis species genome, conducted by Professor Bao Liu’s research team of Northeast Normal University.). We will also review these two articles and share with our readers.
Now, let’s take a glance at the excellent research articles published on 2021 co-authored by BMK and our collaborated facilities.
Plant Genome — Breakthroughs on multi-species.
1.A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes
Collaborated Facility: Henan Agricultural University
Journal: Natural Genetics
Impact Factor: 38.31
In this project, genome of Weining rye, an elite Chinese rye variety, was sequenced. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.
2.Rose without prickle: genomic insights linked to moisture adaptation
Collaborated Facility: Kunming Institute of botany, Chinese Academy of Sciences
Journal: National Science Review
Impact Factor: 17.273
In this project, samples of ‘Basye’s Thornless’ (BT, a prickle-free cultivar of Rosa wichuraiana), ‘Old Blush’ (OB, a founder genotype in rose domestication), their F1 hybrids and BCF1 were collected. And a high-quality reference genome assembly was generated to identify genetic elements related to stem prickle development. The genome size is about 530.6 Mb. To verify the quality of the assembled genome, analysis like genetic map comparison, BUSCO, NGS reads reassembly, comparison with OB haplotype, sequencing base error rate control and genome-wide LTR Assembly Index value check (LAI=20.03) were conducted. This research reveal the complex inheritance pattern and regulatory mechanism of stem prickles and provided us with a foundation and novel resources to study rose biology and mine molecular markers associated with important traits.
3.Whole-Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization
Collaborated Facility: Nanjing Agricultural University
Journal: Advanced Science
Impact Factor: 16.801
This study reported the high-quality genome of a synthetic allotetraploid obtained using interspecific hybridization between cucumber (C. sativus, 2n = 14) and its wild relative species (C. hystrix, 2n = 24) and subsequent chromosome duplication, which is the first fully sequenced synthetic allopolyploid. The assembly of the genome applied the workflow of “PacBio+BioNano+Hi-C+Illumina” sequencing, resulted in genome size of 530.8Mb and contig N50 = 6.5Mb. Reads were assigned to 19 pseudochromosomes and subgenomes. The results indicated that hybridization, rather than genome duplication, causes the majority of genomic changes in both nuclear and cp genomes. It suggested that the fixed heterozygosity provides C.×hytivus with increased stress adaptation. The results provide new insights into plant polyploidy evolution and offer a prospective breeding strategy for future crops.
4.Comparative Genome Analyses Highlight Transposon Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton
Collaborated Facility: Huazhong Agricultural University
Journal: Molecular Biology and Evolution
Impact Factor: 16.242
This project used Nanopore Sequencing to assemble genome of three cotton species namely: Gossypium rotundifolium (K2, genome size = 2.44Gb, contigN50 = 5.33Mb), G. arboreum (A2, genome size = 1.62Gb, contigN50 = 11.69Mb), and G. raimondii (D5, genome size = 0.75Gb, contigN50 = 17.04 Gb). Over 99% of all three genomes were assembled through Hi-C. The results of BUSCO analysis are 92.5%, 93.9% and 95.4% respectively. All these numbers indicated that the three assembly genomes are reference -grade. Comparative genome analyses documented the details of lineage-specific TE amplification contributing to the large genome size differences. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.
5.Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome
Collaborated Facility: CAS Center for Excellence in molecular Plant Sciences
Journal: Nature Communications
Impact Factor: 14.912
This project reported a chromosome-scale assembly of Miscanthus lutarioriparius genome by combining Oxford Nanopore sequencing and Hi-C technologies. The 2.07Gb assembly covers 96.64% of the genome, with contig N50 of 1.71 Mb. About 94.30% of total sequences were anchored into 19 pseudochromosomes. Through comparison with BAC sequence, LAI evaluation, BUSCO evaluation, re-assembly with NGS data, re-assembly of transcriptome data, the genome was evaluated as high-quality and continuity. Allotetraploid origin of the M. lutarioriparius is confirmed using centromeric satellite repeats. Tandem duplicate genes of M. lutarioriparius are functional enriched not only in terms related to stress response, but cell wall biosynthesis. Gene duplicates probably play a role in the C4 photosynthesis and contribute to Miscanthus C4 photosynthesis at low temperature. The research provided important reference for studying perennial plants.
6.A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis
Collaborated Facility: Sichuan University
Journal: Nature Communications
Impact Factor: 14.912
This project reported a high-quality, chromosome-level C. acuminata genome assembly, with genome size of 414.95Mb and contingN50 1.47Mb. We found that C. acuminata experiences an independent whole-genome duplication and numerous genes derive from it are related to camptothecin biosynthesis. The functional divergence of the LAMT gene and positive evolution of two SLAS genes, therefore, both contributed greatly to the camptothecin biosynthesis in C. acuminata. The results emphasized the importance of high-quality genome assembly in identifying genetic changes in the evolutionary origin of a secondary metabolite.
7.Allele-defined genome reveals biallelic differentiation during cassava evolution
Collaborated Facility: Chinese Academy of Tropical Agricultural Sciences
Journal: Molecular Plant
Impact Factor: 13.162
This project assembled a reference genome for cassava with contigN50 1.1Mb using Pacific Biosciences (PacBio) sequencing platform. After evaluation by BUSCO, LAI index, and high-density genetic map, the assembled genome is confirmed as refence-grade. The redundant regions were identified and contigs were anchored onto 18 pseudochromosomes using Hi-C links. This high-quality and allele-defined reference genome for cassava is valuable in identifying divergent bi-alleles on homologous chromosomes, allowing to explore differentiation and expression dominance of bi-alleles and their underlying evolutionary driving forces. It facilitated innovating breeding strategies in cassava and other highly heterozygous crops.
8.Genomic insights into the fast growth of paulownias and the formation of Paulownia witches' broom
Collaborated Facility: Henan Agricultural university
Journal: Molecular Plant
Impact Factor: 13.162
This project assembled a high-quality nuclear genome of Paulownia fortunei, 511.6 Mb in size, with 93.2% of the sequences being anchored to 20 pseudochromosomes. Higher photosynthetic efficiency is achieved through integrating C3 photosynthesis and the crassulacean acid metabolism pathway, which may have contributed to the extremely fast growth habit of paulownia trees. Additional genome sequencing of PaWB phytoplasma, combined with functional analyses,indicated that the effector PaWB-SAP54 directly interacts with Paulownia PfSPLa, which in turn causes the degradation of PfSPLa by the ubiquitin-mediated pathway and leads to the formation of witches’ broom. The data provided significant insights into the biology of paulownias and the regulatory mechanism for the formation of PaWB.
Animal genome – Deep insights of species evolution
1.The genome of Nautilus pompilius illuminates eye evolution and biomineralization
Collaborated Facility: South China Sea Institute of Oceanology, CAS
Journal: Natural Ecology & evolution
Impact Factor: 15.462
This project presented a complete genome for Nautilus pompilius. It has the minimalist genome among sequenced cephalopods, which is 730.58Mb with contigN50 = 1.1Mb. The BUSCO evaluation result is 91.31%. Combined with transcriptome, proteome, gene family and phylogenetic analysis, this genome provided a fundamental reference on cephalopod innovations, such as the pinhole eye and biomineralization. The research indicated that damage on the completeness of Hox gene cluster might be related to the shell disappearing of Mollusks. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The nautilus genome constituted a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.
2.Seadragon genome analysis provides insights into its phenotype and sex determination locus
Collaborated Facility: South China Sea Institute of Oceanology, CAS
Journal: Science Advances
Impact Factor: 14.132
This project de novo–sequenced male and female genomes of the common seadragon (Phyllopteryx taeniolatus) and its closely related species, the alligator pipefish (Syngnathoides biaculeatus). The genome size for Phyllopteryx taeniolatus is ~659 Mb（♂）and ~663 Mb（♀）, with contigN50 of 10.0Mb and 12.1mb. the genome size for Phyllopteryx taeniolatus is 637 Mb（♂）and ~648 Mb（♀）, with contigN50 of 18.0Mb and 21.0Mb. Through phylogenetic analysis, the common seadragon and the alligator pipefish are sister taxon of Syngnathinae, and diverged around 27.3 Ma ago. Transcription profiles from an evolutionary novelty, the leaf-like appendages, show that a set of genes typically involved in fin development have been co-opted as well as an enrichment of tran-scripts for potential tissue repair and immune defense genes. A putative sex–determining locus encoding a male-specific amhr2y gene shared by common seadragon and alligator pipefish was identified. This project provided critical evidence for studies of adaptive evolution.
Post time: Sep-19-2022