Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution

Despite the scientific and medicinal importance of diploid sika deer(Cervus nippon),its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed.To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae,we report,for the first time,a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies,which was anchored to 32 homologous groups with a pair of sex chromosomes(XY).Several expanded genes(RET,PPP2R1A,PPP2R1B,YWHAB,YWHAZ,and RPS6)and positively selected genes(eIF4E,Wnt8A,Wnt9B,BMP4,and TP53)were identified,which could contribute to rapid antler growth without carcinogenesis.A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis.Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer(Cervus elaphus),and the olfactory sensation of sika deer might be more powerful than that of red deer.Obvious inversion regions containing olfactory receptor genes were also identified,which arose since the divergence.In conclusion,the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler,chromosome evolution,and multi-omics research of cervid animals.

Phylogeny and sex chromosome evolution of Palaeognathae

Many paleognaths(ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes.We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of “evolutionary strata”. Nine of the 15 studied species’ sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in the older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate such “defeminization” of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females rather than males, which evolved in their common ancestors.

Karyotypes of field mice of the genus Apodemus (Mammalia： Rodentia) from China

Karyotypes of four Chinese species of field mice of the genus Apodemus were examined,including Apodemus chevrieri （diploid chromosome number,2n=48,fundamental number of autosomal arms,FNa=56）,A.draco （2n=48,FNa=48）,A.ilex （2n=48,FNa=48）,and A.latronum （2n=48,FNa=48）.Karyotypes of A.chevrieri,A.draco,and A.ilex are reported here for the first time,providing useful information for their species taxonomy.Determining the karyotypes of all species of Apodemus in Asia,both in this and previous studies,provides a solid overview of the chromosome evolution and species differentiation of the genus in East Asia.In addition to allopatric speciation,chromosome rearrangements likely played an important role in the formation of the four Apodemus species groups as well as speciation within each group in East Asia.For example,increased centromeric heterochromatin in A.latronum may have contributed to the post-mating reproductive isolation from the A.draco-A.ilex-A.semotus clade.

Chromosomal Engineering of Escherichia coli for Efficient Production of Coenzyme Q_(10)

The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli strain for coenzyme Q10 production. A series of integration expression vectors, pxKC3T5b and pxKT5b, were constructed for chemically inducible chromosomal evolution(multiple copy integration) and replicon-free and markerless chromosomal integration(single copy integration), respectively. A coenzyme Q10 hyper-producer Escherichia coli TBW20134 was constructed by applying chemically inducible chromosomal evolution,replicon-free and markerless chromosomal integration as well as deletion of menaquinone biosynthetic pathway.The engineered E. coli TBW20134 produced 10.7 mg per gram of dry cell mass(DCM) of coenzyme Q10 when supplemented with 0.075 g·L-1of 4-hydroxy benzoic acid; this yield is unprecedented in E. coli and close to that of the commercial producer Agrobacterium tumefaciens. With this strain, the coenzyme Q10 production capacity was very stable after 30 sequential transfers and no antibiotics were required during the fermentation process. The strategy presented may be useful as a general approach for construction of stable production strains synthesizing natural products where various copy numbers for different genes are concerned.

Thirteen Dipterocarpoideae genomes provide insights into their evolution and borneol biosynthesis

Dipterocarpoideae,the largest subfamily of the Dipterocarpaceae,is a dominant component of Southeast Asian rainforests and is widely used as a source of wood,damar resin,medicine,and essential oil.However,many Dipterocarpoideae species are currently on the IUCN Red List owing to severe degradation of their habitats under global climate change and human disturbance.Genetic information regarding these taxa has only recently been reported with the sequencing of four Dipterocarp genomes,providing clues to the function and evolution of these species.Here,we report on 13 high-quality Dipterocarpoideae genome assemblies,ranging in size from 302.6 to 494.8 Mb and representing the five most species-rich genera in Dipterocarpoideae.Molecular dating analyses support the Western Gondwanaland origin of Dipterocarpaceae.Based on evolutionary analysis,we propose a three-step chromosome evolution scenario to describe the karyotypic evolution from an ancestor with six chromosomes to present-day species with 11 and 7 chromosomes.We discovered an expansion of genes encoding cellulose synthase(CesA),which is essential for cellulose biosynthesis and secondary cell-wall formation.We functionally identified five bornyl diphosphate synthase(BPPS)genes,which specifically catalyze the biosynthesis of borneol,a natural medicinal compound extracted from damar resin and oils,thus providing a basis for large-scale production of natural borneol in vitro.

High chromosomal evolutionary dynamics in sleeper gobies(Eleotridae)and notes on disruptive biological factors in Gobiiformes karyotypes(Osteichthyes,Teleostei)

The order Gobiiformes is made up of more than 2200 species,representing one of the most diverse groups among teleost fishes.The biological causes for the tachytelic karyotype evolution of the gobies have not yet been fully studied.Here we expanded cytogenetic data for the Eleotridae family,analyzing the neotropical species Dormitator maculatus,Eleotris pisonis,Erotelis smaragdus,and Guavina guavina.In addition,a meta-analytical approach was followed for elucidating the karyotype diversification versus biological aspects(habitat and egg type)of the Gobiiformes.The species E.smaragdus and E.pisonis present 2n=46 acrocentric chromosomes(NF=46),D.maculatus 2n=46(36sm+4st+6a;NF=86),and G.guavina,the most divergent karyotype,with 2n=52 acrocentric chromosomes(NF=52).Besides numeric and structural diversification in the karyotypes,the mapping of rDNAs and microsatellites also showed noticeable numerical and positional variation,supporting the high chromosomal evolutionary dynamism of these species.In Gobiiformes,karyotype patterns which are more divergent from the basal karyotype(2n=46a)are associated with characteristics less effective to dispersion,such as the benthic habit.These adaptive characteristics,connected with the organization of the repetitive DNA content in the chromosomes,likely play a synergistic role in the remarkable karyotype diversification of this group.

Autotriploid origin of Carassius auratus as revealed by chromosomal locus analysis

In the Dongting water system, the Carassius auratus(Crucian carp) complex is characterized by the coexistence of diploid forms(2n=100, 2n CC) and polyploid forms. Chromosomal and karyotypic analyses have suggested that the polyploid C. auratus has a triploid(3n=150, 3n CC) and a tetraploid origin(4n=200), respectively. However, there is a lack of direct genetic evidence to support this conclusion. In this paper, analysis of the 5S r DNA chromosomal locus revealed that the 3n CC is of triploid origin. Analysis of the species-specific chromosomal centromere locus revealed that 3n CC individuals possess three sets of C. auratus-derived chromosomes. Our results provide direct cytogenetic evidence suggesting that individuals with 150 chromosomes are of autotriploid origin within the C. auratus complex. It marks an important contribution to the study of polyploidization and the evolution of vertebrates.