The animal in the genome: comparative genomics and evolution

Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.     

Chromosome-level genome assembly of an agricultural pest,the rice leaffolder Cnaphalocrocis exigua (Crambidae,Lepidoptera)

The rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera) is an important agricultural pest that damages rice crops and other members of related grass families. C. exigua exhibits a very similar morphological phenotype and feeding behaviour to C. medinalis, another species of rice leaffolder whose genome was recently reported. However, genomic information for C. exigua remains extremely limited. Here, we used a hybrid strategy combining different sequencing technologies, including Illumina, PacBio, 10× Genomics, and Hi – C scaffolding, to generate a high-quality chromosome-level genome assembly of C. exigua. We initially obtained a 798.8 Mb assembly with a contig N50 size of 2.9 Mb, and the N50 size was subsequently increased to 25.7 Mb using Hi – C technology to anchor 1413 scaffolds to 32 chromosomes. We detected a total of 97.7% Benchmarking Universal Single-Copy Orthologues (BUSCO) in the genome assembly, which was comprised of ~52% repetitive sequence and annotated 14,922 protein-coding genes. Of note, the Z and W sex chromosomes were assembled and identified. A comparative genomic analysis demonstrated that despite the high synteny observed between the two rice leaffolders, the species have distinct genomic features associated with expansion and contraction of gene families and selection pressure. In summary, our chromosome-level genome assembly and comparative genomic analysis of C. exigua provide novel insights into the evolution and ecology of this rice insect pests and offer useful information for pest control.     

Plastid genome sequencing,comparative genomics,and phylogenomics: Current status and prospects

Abstract More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies. Based on this unprecedented abundance of data, extensive genomic changes have been revealed in the plastid genomes. Inversion is the most common mechanism that leads to gene order changes. Several inversion events have been recognized as informative phylogenetic markers, such as a 30‐kb inversion found in all living vascular plants minus lycopsids and two short inversions putatively shared by all ferns. Gene loss is a common event throughout plastid genome evolution. Many genes were independently lost or transferred to the nuclear genome in multiple plant lineages. The trnR‐CCG gene was lost in some clades of lycophytes, ferns, and seed plants, and all the ndh genes were absent in parasitic plants, gnetophytes, Pinaceae, and the Taiwan moth orchid. Certain parasitic plants have, in particular, lost plastid genes related to photosynthesis because of the relaxation of functional constraint. The dramatic growth of plastid genome sequences has also promoted the use of whole plastid sequences and genomic features to solve phylogenetic problems. Chloroplast phylogenomics has provided additional evidence for deep‐level phylogenetic relationships as well as increased phylogenetic resolutions at low taxonomic levels. However, chloroplast phylogenomics is still in its infant stage and rigorous analysis methodology has yet to be developed.     

Chromosome-level de novo genome assembly of two conifer-parasitic wasps,Megastigmus duclouxiana and Megastigmus sabinae,reveals genomic imprints of adaptation to hosts

Conifers make up about one third of global forests but are threatened by seed parasitoid wasp species. Many of these wasps belong to the genus Megastigmus, yet little is known about their genomic background. In this study, we provide chromosome-level genome assemblies for two oligophagous conifer parasitoid species of Megastigmus, which represent the first two chromosome-level genomes of the genus. The assembled genomes of Megastigmus duclouxiana and M. sabinae are 878.48 Mb (scaffold N50 of 215.60 Mb) and 812.98 Mb (scaffold N50 of 139.16 Mb), respectively, which are larger than the genome size of most hymenopterans due to the expansion of transposable elements. Expanded gene families highlight the difference in sensory-related genes between the two species, reflecting the difference in their hosts. We further found that these two species have fewer family members but more single-gene duplications than polyphagous congeners in the gene families of ATP-binding cassette transporter (ABC), cytochrome P450 (P450) and olfactory receptors (OR). These findings shed light on the pattern of adaptation to a narrow spectrum of hosts in oligophagous parasitoids. Our findings suggest potential drivers underlying genome evolution and parasitism adaptation, and provide valuable resources for understanding the ecology, genetics and evolution of Megastigmus, as well as for the research and biological control of global conifer forest pests.     

Plastid genome sequencing,comparative genomics,and phylogenomics:Current status and prospects

More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies.Based on this unprecedented abundance of data,extensive genomic changes have been revealed in the plastid genomes.Inversion is the most common mechanism that leads to gene order changes.Several inversion events have been recognized as informative phylogenetic markers,such as a 30-kb inversion found in all living vascular plants minus lycopsids and two short inversions putat...     

Origin and evolution of the major histocompatibility complex class I region in eutherian mammals

Major histocompatibility complex (MHC) genes in vertebrates are vital in defending against pathogenic infections. To gain new insights into the evolution of MHC Class I (MHCI) genes and test competing hypotheses on the origin of the MHCI region in eutherian mammals, we studied available genome assemblies of nine species in Afrotheria, Xenarthra, and Laurasiatheria, and successfully characterized the MHCI region in six species. The following numbers of putatively functional genes were detected: in the elephant, four, one, and eight in the extended class I region, and κ and β duplication blocks, respectively; in the tenrec, one in the κ duplication block; and in the four bat species, one or two in the β duplication block. Our results indicate that MHCI genes in the κ and β duplication blocks may have originated in the common ancestor of eutherian mammals. In the elephant, tenrec, and all four bats, some MHCI genes occurred outside the MHCI region, suggesting that eutherians may have a more complex MHCI genomic organization than previously thought. Bat‐specific three‐ or five‐amino‐acid insertions were detected in the MHCI α1 domain in all four bats studied, suggesting that pathogen defense in bats relies on MHCIs having a wider peptide‐binding groove, as previously assayed by a bat MHCI gene with a three‐amino‐acid insertion showing a larger peptide repertoire than in other mammals. Our study adds to knowledge on the diversity of eutherian MHCI genes, which may have been shaped in a taxon‐specific manner.     

中国濒危兽类保护基因组学和宏基因组学研究进展与展望

揭示濒危兽类的演化历史、濒危机制及适应性演化策略,是保护生物学关注的重大科学问题。近十几年来,高通量测序技术的不断发展以及多学科交叉融合,为揭示濒危物种的演化历史、遗传结构、适应性演化及其与肠道微生物的协同演化的分子机制提供了重要的技术支撑,由此产生了保护基因组学和保护宏基因组学两个分支学科,为野生动物尤其是濒危动物的保护生物学研究提供了新的方向与思路。本文综述了我国在保护基因组学和保护宏基因组学领域取得的重要进展,并展望未来的发展趋势,以期进一步推动我国濒危兽类保护生物学的发展。     

An orphan gyrB in the Mycobacterium smegmatis genome uncovered by comparative genomics

DNA gyrase is an essential topoisomerase found in all bacteria. It is encoded bygyrB andgyrA genes. These genes are organized differently in different bacteria. Direct comparison ofMycobacterium tuberculosis andMycobacterium smegmatis genomes reveals presence of an additionalgyrB inM. smegmatis flanked by novel genes. Analysis of the amino acid sequence of GyrB from different organisms suggests that the orphan GyrB inM. smegmatis may have an important cellular role.     

Genomes of extremophile crucifers: new platforms for comparative genomics and beyond

ABSTRACT: Recent reports describe the genome sequencing of Thellungiella salsuginea and Thellungiella parvula, two extremophile crucifers closely related to the stress-sensitive model plant Arabidopsis thaliana.     

Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato

Comparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race-specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co-evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown.     

杀虫剂抗性: 遗传学、基因组学及应用启示

杀虫剂抗性已成为害虫防治工作需要解决的一个重要问题,也是一种人为的、自然选择的重要的进化现象,开展抗药性的研究不仅为抗性的监测、治理和农药工业的发展提供科学参考,还可以揭示生物进化的一些基本规律。在过去的10年,昆虫对许多化学杀虫剂抗药性的分子基础得到了进一步阐明,已从果蝇Drosophila melanogaster中克隆了杀虫剂的靶标基因,还查明了一些害虫的与抗性相关联的基因突变。最近,随着经注释的昆虫基因组的出现,由复杂多基因酶系如酯酶、细胞色素P450酶及谷胱甘肽S-转移酶介导的抗性的机制有了突破性的进展,有关杀虫剂抗性的进化以及抗性基因的传播模式也逐步得到揭示。基因组技术在揭示昆虫其他可能的抗药性机制以及在发现新的杀虫剂靶标方面将发挥更大的作用。     

一株新的产吡咯喹啉醌甲基营养菌全基因组测序和比较基因组学分析

【背景】由于甲基营养菌被发现的时间较短,而且可以生产吡咯喹啉醌(pyrroloquinoline quinone,PQQ)的甲基杆菌属细菌只有少数菌株的全基因组序列被公布,增加了该类细菌基因组学和生物代谢途径研究的难度。【目的】将本实验室筛选的PQQ生产菌经多种诱变方式处理,用于提高PQQ的发酵产量。对高产突变菌株进行全基因组解析,以探究甲基杆菌PQQ合成的分子机制,为后续分子育种提供序列背景信息。【方法】将野生型PQQ生产菌株进行紫外诱变、亚硝基胍诱变、甲基磺酸乙酯诱变、硫酸二乙酯诱变和紫外-氯化锂复合诱变。将突变菌株利用PromethION三代测序平台和MGISEQ-2000二代测序平台测序,然后进行组装和功能注释。组装得到的全基因组序列与模式菌株扭脱甲基杆菌AM1 (Methylobacterium extorquens AM1)进行比较基因组学分析。【结果】经11轮诱变获得一株突变菌株NI91,其PQQ产量为19.49mg/L,相较原始菌株提高44.91%。突变菌株NI91的基因组由一个5 409 262 bp的染色体组成,共编码4 957个蛋白,与模式菌株M. extorqu...     

A chromosome-level reference genome and pangenome for barn swallow population genomics

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副干酪乳杆菌PC-01全基因组测序及不同副干酪乳杆菌菌株比较基因组学分析

【背景】副干酪乳杆菌(Lactobacillus paracasei)作为乳酸菌中重要菌种之一,常被认为是优良益生菌开发的潜在资源。【目的】以L.paracasei PC-01和L.paracasei Zhang为例,分析不同L.paracasei的基因组差异和遗传背景,为菌株的鉴定和开发奠定基础。【方法】采用PacBioSMRT三代测序技术对L.paracasei PC-01进行全基因组测序,结合2株L.paracasei模式菌株和公开的36株全基因组数据,通过比较基因组学方法揭示39株L.paracasei菌株之间的差异。【结果】L.paracasei PC-01基因组不包含质粒,染色体大小为2 829 251 bp,GC含量为46.64%;L.paracasei Zhang包含一个质粒基因组大小为2 898 456 bp,GC含量为46.51%;不同L.paracasei菌株基因组大小、质粒数及GC含量均存在一定差异。L.paracasei群体为开放式基因组,基因组具有高度多样性。基于核心基因构建系统发育树对于L.paracasei种内区分效果最好,L.paracasei PC-...     

Rapid identification of the Leptosphaeria maculans avirulence gene AvrLm2 using an intraspecific comparative genomics approach

Five avirulence genes from Leptosphaeria maculans, the causal agent of blackleg of canola (Brassica napus), have been identified previously through map‐based cloning. In this study, a comparative genomic approach was used to clone the previously mapped AvrLm2. Given the lack of a presence–absence gene polymorphism coincident with the AvrLm2 phenotype, 36 L. maculans isolates were resequenced and analysed for single‐nucleotide polymorphisms (SNPs) in predicted small secreted protein‐encoding genes present within the map interval. Three SNPs coincident with the AvrLm2 phenotype were identified within LmCys1, previously identified as a putative effector‐coding gene. Complementation of a virulent isolate with LmCys1, as the candidate AvrLm2 allele, restored the avirulent phenotype on Rlm2‐containing B. napus lines. AvrLm2 encodes a small cysteine‐rich protein with low similarity to other proteins in the public databases. Unlike other avirulence genes, AvrLm2 resides in a small GC island within an AT‐rich isochore of the genome, and was never found to be deleted completely in virulent isolates.