Genomic Mutations Within the Host Microbiome: Adaptive Evolution or Purifying Selection

Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.

Inbreeding and genetic load in a pair of sibling grouse species:Tetrastes sewersowi and T.bonasia

Genetic load and inbreeding are recognized as important factors to be considered in conservation programs.Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation.We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both.We found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(T.bonasia).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse.Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of birds.Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels.Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse.These results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse.However,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.

MHC Class I Exon 4 in the Multiocellated Racerunners(Eremias multiocellata): Polymorphism, Duplication and Selection

The major histocompatibility complex （MHC） is a dynamic genetic region with an essential role in the adaptive immunity of jawed vertebrates. The MHC polymorphism is affected by many processes such as birth-and- death evolution, gene conversion, and concerted evolution. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. However, the investigation of this region in nonavian reptiles is still in its infancy. We present the first characterization of MHC class I genes in a species from the family Lacertidae. We assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 4 among 37 individuals of Eremias multiocellata from a population in Lanzhou, China. We generated 67 distinct DNA sequences using cloning and sequencing methods, and identified 36 putative functional variants as well as two putative pseudogene-variants. We found the number of variants within an individual varying between two and seven, indicating that there are at least four MHC class I loci in this species. Gene duplication plays a role in increasing copy numbers of MHC genes and allelic diversity in this species. The class I exon 4 sequences are characteristic of low nucleotide diversity. No signal of recombination is detected, but purifying selection is detected in β2-microglobulin interaction sites and some other silent sites outside of the function-constraint regions. Certain identical alleles are shared by Eremias multiocellata and E. przewalskii and E. brenchleyi, suggesting trans-species polymorphism. The data are compatible with a birth-and-death model of evolution.

Complete Mitochondrial Genome of the Steppe Ribbon Racer(Psammophis lineolatus):The First Representative from the Snake Family Psammophiidae and its Phylogenetic Implications

Comparisons of vertebrate mitochondrial genomes(mitogenomes)may yield significant insights into the evolution of organisms and genomes.However,no complete mitogenome from the snake family Psammophiidae has been reported.In this study,we sequenced and annotated the complete mitogenome of Psammophis lineolatus,representing the first mitogenome of Psammophiidae.The total length is 17166 bp,consisting of 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),two ribosomal RNAs(12 S rRNA and16 S rRNA),and duplicate control regions(CRs).This gene arrangement belongs to the TypeⅢpattern,which is a widely shared gene order in Alethinophidian snakes.All tRNAs exhibit cloverleaf structures with the exception of tRNA-Ser^(AGY) and tRNA-Pro,which lack a dihydrouridine(DHU)arm/stem and TΨC loop,respectively.The 13 PCGs include five start codons(ATG,GTG,ATA,ATT,and ATC),two complete stop codons(TAA and AGG),and two incomplete stop codon(T--and TA-).In addition,the Ka/Ks ratios indicate that all PCGs had undergone a strong purifying selection.Four types of CR domains rearrangement occurred among eight species of Elapoidea.The phylogenetic reconstructions with both Bayesian inference and maximum likelihood methods support the placement of Psammophiidae in the Elapoidea superfamily,with Homalopsidae being the sister taxon to Elapoidea and Colubroidea.However,the sister taxon of Psammophiidae is unclear due to the availability of Elapoidea mitogenomes being limited to the family Elapidae.More mitogenomes from different taxonomic groups in Elapoidea are needed to better understand the phylogenetic relationships within Elapoidea.

Natural selection maintains the transcribed LTR retrotransposons in Nosema bombycis

Eight intact LTR retrotransposons （Nbr1-Nbr8） have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements （Nbr9-Nbr14） identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions （Nbr12）, deletions （Nbrll） and in-frame stop codons in coding regions （Nbr9） were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bornbycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbrll is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbrll retrotransposon. Unlike other transposable elements, Nbrll has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants

Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster(BGC)in maize.Data mining of 41 high-quality grass genomes identified complete Bx clusters(containing genes Bx1–Bx5 and Bx8)in three genera(Zea,Echinochloa,and Dichanthelium)of Panicoideae and partial clusters in Triticeae.The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes.An ancient Bx cluster that included additional Bx genes(e.g.,Bx6)is presumed to have been present in ancestral Panicoideae.The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer(HT)from the ancestral Panicoideae and later separated into multiple segments on different chromosomes.Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae,as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays,moved to other chromosomes in Echinochloa,and even lost in Dichanthelium.Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family.This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.