Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments DOI Creative Commons
Zihao Yuan, Shikai Liu, Tao Zhou

et al.

BMC Genomics, Journal Year: 2018, Volume and Issue: 19(1)

Published: Feb. 13, 2018

Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the repetitive fish genomes, we conducted a comparative analysis 52 species 22 orders relation to living aquatic environments. The various genomes were found be positively correlated with genome sizes, few exceptions. More importantly, there appeared specific enrichment between some element categories habitat. Specifically, class II transposons appear more abundant freshwater bony than marine when phylogenetic relationship is not considered. In contrast, harbor tandem repeats species. addition, I primitive such as cartilaginous and lamprey fish. enriched association habitats suggests importance potential adaptation due restriction limited sequenced species, further needs done alleviate biases.

Language: Английский

Research advances in the genomics and applications for molecular breeding of aquaculture animals DOI
Xinxin You, Xinxin Shan, Qiong Shi

et al.

Aquaculture, Journal Year: 2020, Volume and Issue: 526, P. 735357 - 735357

Published: April 10, 2020

Language: Английский

Citations

115
Concomitant loss of NDH complex‐related genes within chloroplast and nuclear genomes in some orchids DOI Open Access
Choun‐Sea Lin, Jeremy J.W. Chen, Chi‐Chou Chiu

et al.

The Plant Journal, Journal Year: 2017, Volume and Issue: 90(5), P. 994 - 1006

Published: March 4, 2017

The chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of about 30 subunits from both the nuclear and genomes is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale catenatum, 11 genome-encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh completely lost in these orchids or they transferred retained genome. Further, assessed nucleus-encoded NDH-related can be lost, resulting absence NDH complex. Comparative analyses genome Apostasia odorata, an orchid species with a complete complement which represents sister lineage to all other three published sequences for P. D. are missing genes, indicated that copies not present any four genomes. This observation suggests necessary genomic/transcriptomic currently available plastid transcriptome data showed 47 out 660 photoautotrophic plants heterotrophic plastid-encoded exhibit no evidence maintenance Our indicate plant species. loss may increase probability transition life history.

Language: Английский

Citations

113
Metagenomic reconstructions of gut microbial metabolism in weanling pigs DOI Creative Commons
Weilan Wang, Huifeng Hu, R. T. Zijlstra

et al.

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: March 26, 2019

The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability harvest energy dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics 72). Time wheat content explained most variation microbiota as assessed by pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic 1 archaeal phylum. Analysis these revealed starch fermentation is carried out consortium Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) Bacteroidetes periplasmic neopullulanase α-glucosidase (GH97). Fructans were degraded GH32 enzymes Bacteriodetes Lactobacillus. Lactose β-galactosidases (GH2 GH42) was identified Firmicutes. In conclusion, assembly first reference for swine intestinal allowed identification key contributors degradation starch, fructans, lactose. Microbial consortia are responsible glycans differ substantially degrade same humans. Our thus enables improvement feeding models with higher efficiency better pathogen control

Language: Английский

Citations

108
Microbial metabolites regulate host lipid metabolism through NR5A–Hedgehog signalling DOI
Chih-Chun Lin, Meng C. Wang

Nature Cell Biology, Journal Year: 2017, Volume and Issue: 19(5), P. 550 - 557

Published: April 24, 2017

Language: Английский

Citations

99
Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments DOI Creative Commons
Zihao Yuan, Shikai Liu, Tao Zhou

et al.

BMC Genomics, Journal Year: 2018, Volume and Issue: 19(1)

Published: Feb. 13, 2018

Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the repetitive fish genomes, we conducted a comparative analysis 52 species 22 orders relation to living aquatic environments. The various genomes were found be positively correlated with genome sizes, few exceptions. More importantly, there appeared specific enrichment between some element categories habitat. Specifically, class II transposons appear more abundant freshwater bony than marine when phylogenetic relationship is not considered. In contrast, harbor tandem repeats species. addition, I primitive such as cartilaginous and lamprey fish. enriched association habitats suggests importance potential adaptation due restriction limited sequenced species, further needs done alleviate biases.

Language: Английский

Citations

91