Today in 16s Sequencing with MR DNA
161. J Nutr. 2016 Feb;146(2):200-8. doi: 10.3945/jn.115.220152. Epub 2015 Dec 23.
Dietary Isomers of Sialyllactose Increase Ganglioside Sialic Acid Concentrations
in the Corpus Callosum and Cerebellum and Modulate the Colonic Microbiota of
Jacobi SK(1), Yatsunenko T(2), Li D(3), Dasgupta S(3), Yu RK(3), Berg BM(4),
Chichlowski M(5), Odle J(6).
(1)Laboratory of Developmental Nutrition, Department of Animal Science, North
Carolina State University, Raleigh, NC; (2)Second Genome, Inc., South San
Francisco, CA; (3)Institute of Molecular Medicine and Genetics, Georgia Regents
University, Augusta, GA; (4)Mead Johnson Pediatric Nutrition Institute,
Evansville, IN; and Division of Nutritional Sciences, University of Illinois,
Urbana, IL. (5)Mead Johnson Pediatric Nutrition Institute, Evansville, IN; and.
(6)Laboratory of Developmental Nutrition, Department of Animal Science, North
Carolina State University, Raleigh, NC; email@example.com.
BACKGROUND: Sialyllactose is a key human milk oligosaccharide and consists of
sialic acid (SA) bound to a lactose molecule. Breastfed infants have increased
accumulation of ganglioside-bound SA compared with formula-fed infants.
OBJECTIVE: This study aimed to determine whether different isomers of
sialyllactose enrich brain SA and modulate the microbiome of developing neonatal
METHODS: Day-old pigs were randomly allocated to 6 diets (control, 2 or 4 g
3'-sialyllactose/L, 2 or 4 g 6'-sialyllactose/L, or 2 g polydextrose/L + 2 g
galacto-oligosaccharides/L; n = 9) and fed 3 times/d for 21 d. Pigs were killed,
and the left hemisphere of the brain was dissected into cerebrum, cerebellum,
corpus callosum, and hippocampus regions. SA was determined by using a modified
periodic acid-resorcinol reaction. Microbial composition of the intestinal
digesta was analyzed with the use of 16S ribosomal DNA Illumina sequencing.
RESULTS: Dietary sialyllactose did not affect feed intake, growth, or fecal
consistency. Ganglioside-bound SA in the corpus callosum of pigs fed 2 g
3'-sialyllactose or 6'-sialyllactose/L increased by 15% in comparison with
control pigs. Similarly, ganglioside-bound SA in the cerebellum of pigs fed 4 g
3'-sialyllactose/L increased by 10% in comparison with control pigs. Significant
(P < 0.05, Adonis Test) microbiome differences were observed in the proximal and
distal colons of piglets fed control compared with 4-g 6'-sialyllactose/L
formulas. Differences were attributed to an increase in bacterial taxa belonging
to species Collinsella aerofaciens (phylum Actinobacteria), genera Ruminococcus
and Faecalibacterium (phylum Firmicutes), and genus Prevotella (phylum
Bacteroidetes) (Wald test, P < 0.05, DeSeq2) compared with piglets fed the
control diet. Taxa belonging to families Enterobacteriaceae and Enterococcaceae
(phylum Proteobacteria), as well as taxa belonging to family Lachnospiraceae and
order Lactobacillales (phylum Firmicutes), were 2.3- and 4-fold lower,
respectively, in 6'-sialyllactose-fed piglets than in controls.
CONCLUSIONS: Supplementation of formula with 3'- or 6'-sialyllactose can enrich
ganglioside SA in the brain and modulate gut-associated microbiota in neonatal
pigs. We propose 2 potential routes by which sialyllactose may positively affect
the neonate: serving as a source of SA for neurologic development and promoting
© 2016 American Society for Nutrition.
PMID: 26701794 [PubMed - indexed for MEDLINE]
62. PLoS One. 2016 Mar 16;11(3):e0151214. doi: 10.1371/journal.pone.0151214.
Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from
the Metagenome of an Electrosynthetic Microbiome.
Ross DE(1), Marshall CW(2), May HD(2), Norman RS(1).
(1)Department of Environmental Health Sciences, Arnold School of Public Health,
University of South Carolina, Columbia, South Carolina, United States of America.
(2)Department of Microbiology & Immunology, Marine Biomedicine & Environmental
Science Center, Medical University of South Carolina, Charleston, South Carolina,
United States of America.
Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and
contain metabolic versatility that enables reduction of a wide range of electron
acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and
nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from
the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of
this organism in microbial electrosynthesis systems suggest it plays an important
role in reactor stability and performance. Understanding why this organism is
present and elucidating its genetic repertoire provide a genomic and ecological
foundation for future studies where Sulfurospirillum are found, especially in
electrode-associated communities. Metabolic comparisons and in-depth analysis of
unique genes revealed potential ecological niche-specific capabilities within the
Sulfurospirillum genus. The functional similarities common to all genomes, i.e.,
core genome, and unique gene clusters found only in a single genome were
identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide
identity, the Sulfurospirillum draft genome was found to be most closely related
to Sulfurospirillum cavolei. Characterization of the draft genome described
herein provides pathway-specific details of the metabolic significance of the
newly described Sulfurospirillum cavolei MES and, importantly, yields insight to
the ecology of the genus as a whole. Comparison of eleven sequenced
Sulfurospirillum genomes revealed a total of 6246 gene clusters in the
pan-genome. Of the total gene clusters, 18.5% were shared among all eleven
genomes and 50% were unique to a single genome. While most Sulfurospirillum spp.
reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode
for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide
reductase, suggesting a utility for this genus in reduction of the nitrous oxide,
and as a potential sink for this potent greenhouse gas.
PMID: 26983005 [PubMed - indexed for MEDLINE]
63. Environ Microbiol. 2014 Sep;16(9):2879-90. doi: 10.1111/1462-2920.12217. Epub
2013 Aug 6.
Complete genome of a new Firmicutes species belonging to the dominant human
colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a
selective capacity to utilize plant glucans.
Wegmann U(1), Louis P, Goesmann A, Henrissat B, Duncan SH, Flint HJ.
(1)Gut Health and Food Safety Programme, Institute of Food Research, Norwich
Research Park, Norwich, NR4 7UA, UK.
The recently isolated bacterial strain 80/3 represents one of the most abundant
16S rRNA phylotypes detected in the healthy human large intestine and belongs to
the Ruminococcaceae family of Firmicutes. The completed genome sequence reported
here is the first for a member of this important family of bacteria from the
human colon. The genome comprises two large chromosomes of 2.24 and 0.73 Mbp,
leading us to propose the name Ruminococcus bicirculans for this new species.
Analysis of the carbohydrate active enzyme complement suggests an ability to
utilize certain hemicelluloses, especially β-glucans and xyloglucan, for growth
that was confirmed experimentally. The enzymatic machinery enabling the
degradation of cellulose and xylan by related cellulolytic ruminococci is however
lacking in this species. While the genome indicated the capacity to synthesize
purines, pyrimidines and all 20 amino acids, only genes for the synthesis of
nicotinate, NAD+, NADP+ and coenzyme A were detected among the essential vitamins
and co-factors, resulting in multiple growth requirements. In vivo, these growth
factors must be supplied from the diet, host or other gut microorganisms. Other
features of ecological interest include two type IV pilins, multiple
extracytoplasmic function-sigma factors, a urease and a bile salt hydrolase.
© 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.
PMID: 23919528 [PubMed - indexed for MEDLINE]
64. Epidemiol Infect. 2016 Jan;144(1):123-37. doi: 10.1017/S0950268815000965. Epub
2015 Jun 11.
Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women.
Dareng EO(1), Ma B(2), Famooto AO(1), Akarolo-Anthony SN(1), Offiong RA(3),
Olaniyan O(4), Dakum PS(1), Wheeler CM(5), Fadrosh D(2), Yang H(2), Gajer P(2),
Brotman RM(2), Ravel J(2), Adebamowo CA(6).
(1)Office of Strategic Information,Research and Training,Institute of Human
Virology,Abuja,Nigeria. (2)Institute for Genome Sciences,University of Maryland
School of Medicine,Baltimore,MD,USA. (3)University of Abuja Teaching
Hospital,Gwagwalada,Nigeria. (4)National Hospital,Abuja,Nigeria. (5)Department of
Pathology,University of New Mexico Health Sciences Centre,Albuquerque,NM,USA.
(6)Department of Nutrition,Harvard School of Public Health,Boston,MA,USA.
In this study, we evaluated the association between high-risk human
papillomavirus (hrHPV) and the vaginal microbiome. Participants were recruited in
Nigeria between April and August 2012. Vaginal bacterial composition was
characterized by deep sequencing of barcoded 16S rRNA gene fragments (V4) on
Illumina MiSeq and HPV was identified using the Roche Linear Array® HPV
genotyping test. We used exact logistic regression models to evaluate the
association between community state types (CSTs) of vaginal microbiota and hrHPV
infection, weighted UniFrac distances to compare the vaginal microbiota of
individuals with prevalent hrHPV to those without prevalent hrHPV infection, and
the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize
bacteria associated with prevalent hrHPV infection. We observed four CSTs: CST
IV-B with a low relative abundance of Lactobacillus spp. in 50% of participants;
CST III (dominated by L. iners) in 39·2%; CST I (dominated by L. crispatus) in
7·9%; and CST VI (dominated by proteobacteria) in 2·9% of participants. LEfSe
analysis suggested an association between prevalent hrHPV infection and a
decreased abundance of Lactobacillus sp. with increased abundance of anaerobes
particularly of the genera Prevotella and Leptotrichia in HIV-negative women (P <
0·05). These results are hypothesis generating and further studies are required.
PMID: 26062721 [PubMed - indexed for MEDLINE]
65. PLoS One. 2016 Mar 4;11(3):e0149998. doi: 10.1371/journal.pone.0149998.
Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum
Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease.
Hogan DA(1), Willger SD(1), Dolben EL(1), Hampton TH(1), Stanton BA(1), Morrison
HG(2), Sogin ML(2), Czum J(3), Ashare A(4).
(1)Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover,
NH, United States of America. (2)Josephine Bay Paul Center for Comparative
Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA,
United States of America. (3)Department of Radiology, Dartmouth-Hitchcock Medical
Center, Lebanon, NH, United States of America. (4)Pulmonary and Critical Care
Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of
Individuals with cystic fibrosis (CF) often acquire chronic lung infections that
lead to irreversible damage. We sought to examine regional variation in the
microbial communities in the lungs of individuals with mild-to-moderate CF lung
disease, to examine the relationship between the local microbiota and local
damage, and to determine the relationships between microbiota in samples taken
directly from the lung and the microbiota in spontaneously expectorated sputum.
In this initial study, nine stable, adult CF patients with an FEV1>50% underwent
regional sampling of different lobes of the right lung by bronchoalveolar lavage
(BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were
obtained from six of the nine subjects immediately prior to the procedure.
Microbial community analysis was performed on DNA extracted from these samples
and the extent of damage in each lobe was quantified from a recent CT scan. The
extent of damage observed in regions of the right lung did not correlate with
specific microbial genera, levels of community diversity or composition, or
bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from
different regions of the lung contained similar microbial communities. In eight
out of nine subjects, PB samples from different regions of the lung were also
similar in microbial community composition, and were similar to microbial
communities in BAL fluid from the same lobe. Microbial communities in PB samples
were more diverse than those in BAL samples, suggesting enrichment of some taxa
in mucus plugs. To our knowledge, this study is the first to examine the
microbiota in different regions of the CF lung in clinically stable individuals
with mild-to-moderate CF-related lung disease.
PMID: 26943329 [PubMed - indexed for MEDLINE]
66. Appl Microbiol Biotechnol. 2014 Apr;98(7):3317-26. doi:
10.1007/s00253-013-5402-z. Epub 2013 Dec 5.
Tracking human sewage microbiome in a municipal wastewater treatment plant.
Cai L(1), Ju F, Zhang T.
(1)Environmental Biotechnology Laboratory, Department of Civil Engineering, The
University of Hong Kong, Hong Kong, SAR, China.
Human sewage pollution is a major threat to public health because sewage always
comes with pathogens. Human sewage is usually received and treated by wastewater
treatment plants (WWTPs) to control pathogenic risks and ameliorate environmental
health. However, untreated sewage that flows into water environments may cause
serious waterborne diseases, as reported in India and Bangladesh. To examine the
fate of the human sewage microbiome in a local municipal WWTP of Hong Kong, we
used massively parallel sequencing of 16S rRNA gene to systematically profile
microbial communities in samples from three sections (i.e., influent, activated
sludge, and effluent) obtained monthly throughout 1 year. The results indicated
that: (1) influent sewage bacterial profile reflected the human microbiome; (2)
human gut bacterial community was the dominant force shaping influent sewage
bacterial profile; (3) most human sewage bacteria could be effectively removed by
the WWTP; (4) a total of 75 genera were profiled as potentially pathogenic
bacteria, most of which were still present in the effluent although at a very low
level; (5) a grouped pattern of bacterial community was observed among the same
section samples but a dispersed pattern was found among the different section
samples; and (6) activated sludge was less affected by the influent sewage
bacteria, but it showed a significant impact on the effluent bacteria. All of
these findings provide novel insights toward a mechanistic understanding of the
fate of human sewage microbiome in the WWTP.
PMID: 24305737 [PubMed - indexed for MEDLINE]
67. BMC Genomics. 2013 Oct 1;14:669. doi: 10.1186/1471-2164-14-669.
Gut microbiota dysbiosis and bacterial community assembly associated with
cholesterol gallstones in large-scale study.
Wu T(1), Zhang Z, Liu B, Hou D, Liang Y, Zhang J, Shi P.
(1)State Key Laboratory of Genetic Resources and Evolution, Laboratory of
Evolutionary & Functional Genomics, Kunming Institute of Zoology, Chinese Academy
of Sciences, Kunming 650223, Yunnan, China. firstname.lastname@example.org.
BACKGROUND: Elucidating gut microbiota among gallstone patients as well as the
complex bacterial colonization of cholesterol gallstones may help in both the
prediction and subsequent lowered risk of cholelithiasis. To this end, we studied
the composition of bacterial communities of gut, bile, and gallstones from 29
gallstone patients as well as the gut of 38 normal individuals, examining and
analyzing some 299, 217 bacterial 16S rRNA gene sequences from 120 samples.
RESULTS: First, as compared with normal individuals, in gallstone patients there
were significant (P < 0.001) increases of gut bacterial phylum Proteobacteria and
decreases of three gut bacterial genera, Faecalibacterium, Lachnospira, and
Roseburia. Second, about 70% of gut bacterial operational taxonomic units (OTUs)
from gallstone patients were detectable in the biliary tract and bacteria
diversity of biliary tract was significantly (P < 0.001) higher than that of gut.
Third, analysis of the biliary tract core microbiome (represented by 106 bacteria
OTUs) among gallstone patients showed that 33.96% (36/106) of constituents can be
matched to known bacterial species (15 of which have publicly available genomes).
A genome-wide search of MDR, BSH, bG, and phL genes purpotedly associated with
the formation of cholesterol gallstones showed that all 15 species with known
genomes (e.g., Propionibacterium acnes, Bacteroides vulgates, and Pseudomonas
putida) contained at least contained one of the four genes. This finding could
potentially provide underlying information needed to explain the association
between biliary tract microbiota and the formation of cholesterol gallstones.
CONCLUSIONS: To the best of our knowledge, this is the first study to discover
gut microbiota dysbiosis among gallstone patients, the presence of which may be a
key contributor to the complex bacteria community assembly linked with the
presence of cholesterol gallstones. Likewise, this study also provides the first
large-scale glimpse of biliary tract microbiota potentially associated with
cholesterol gallstones. Such a characterization of the biliary tract core
microbiome has potentially important biological and medical implications
regarding the role of bacteria in the formation cholesterol gallstones.
PMID: 24083370 [PubMed - indexed for MEDLINE]
PLoS One. 2016 Sep 19;11(9):e0162659. doi: 10.1371/journal.pone.0162659. eCollection 2016.
Yu S1, Ding L1, Luo R1, Li X1, Yang J1, Liu H1, Cong L1, Ran C1.
Dialeurodes citri is a major pest in citrus producing areas, and large-scale outbreaks have occurred increasingly often in recent years. Lecanicillium attenuatum is an important entomopathogenic fungus that can parasitize and kill D. citri. We separated the fungus from corpses of D. citri larvae. However, the sound immune defense system of pests makes infection by an entomopathogenic fungus difficult. Here we used RNA sequencing technology (RNA-Seq) to build a transcriptome database for D. citri and performed digital gene expression profiling to screen genes that act in the immune defense of D. citri larvae infected with a pathogenic fungus. De novo assembly generated 84,733 unigenes with mean length of 772 nt. All unigenes were searched against GO, Nr, Swiss-Prot, COG, and KEGG databases and a total of 28,190 (33.3%) unigenes were annotated. We identified 129 immunity-related unigenes in transcriptome database that were related to pattern recognition receptors, information transduction factors and response factors. From the digital gene expression profile, we identified 441 unigenes that were differentially expressed in D. citri infected with L. attenuatum. Through calculated Log2Ratio values, we identified genes for which fold changes in expression were obvious, including cuticle protein, vitellogenin, cathepsin, prophenoloxidase, clip-domain serine protease, lysozyme, and others. Subsequent quantitative real-time polymerase chain reaction analysis verified the results. The identified genes may serve as target genes for microbial control of D. citri.
PMID: 27644092 DOI: 10.1371/journal.pone.0162659
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Sci Rep. 2016 Sep 19;6:33660. doi: 10.1038/srep33660.
Yaakop AS1, Chan KG2, Ee R2, Lim YL2, Lee SK2, Manan FA1, Goh KM1.
Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.
PMID: 27641516 DOI: 10.1038/srep33660
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J Oral Microbiol. 2016 Sep 16;8:32383. doi: 10.3402/jom.v8.32383. eCollection 2016.
Dame-Teixeira N1, Parolo CC2, Maltz M2, Tugnait A3, Devine D3, Do T4.
The studies of the distribution of Actinomyces spp. on carious and non-carious root surfaces have not been able to confirm the association of these bacteria with root caries, although they were extensively implicated as a prime suspect in root caries.
The aim of this study was to observe the gene expression of Actinomyces spp. in the microbiota of root surfaces with and without caries.
The oral biofilms from exposed sound root surface (SRS; n=10) and active root caries (RC; n=30) samples were collected. The total bacterial RNA was extracted, and the mRNA was isolated. Samples with low RNA concentration were pooled, yielding a final sample size of SRS=10 and RC=9. Complementary DNA (cDNA) libraries were prepared and sequenced on an Illumina(®) HiSeq 2500 system. Sequence reads were mapped to eight Actinomyces genomes. Count data were normalized using DESeq2 to analyse differential gene expression applying the Benjamini-Hochberg correction (false discovery rate [FDR]<0.001).
Actinomyces spp. had similar numbers of reads (Mann-Whitney U-test; p>0.05), except for Actinomyces OT178 (p=0.001) and Actinomyces gerencseriae (p=0.004), which had higher read counts in the SRS. Genes that code for stress proteins (clp, dnaK, and groEL), enzymes of glycolysis pathways (including enolase and phosphoenolpyruvate carboxykinase), adhesion (Type-2 fimbrial and collagen-binding protein), and cell growth (EF-Tu) were highly - but not differentially (p>0.001) - expressed in both groups. Genes with the most significant upregulation in RC were those coding for hypothetical proteins and uracil DNA glycosylase (p=2.61E-17). The gene with the most significant upregulation in SRS was a peptide ABC transporter substrate-binding protein (log2FC=-6.00, FDR=2.37E-05).
There were similar levels of Actinomyces gene expression in both sound and carious root biofilms. These bacteria can be commensal in root surface sites but may be cariogenic due to survival mechanisms that allow them to exist in acid environments and to metabolize sugars, saving energy.
Actinomyces spp.; RNA-seq; differential expression; root caries; transcriptome
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Comp Biochem Physiol Part D Genomics Proteomics. 2016 Aug 28;20:101-110. doi: 10.1016/j.cbd.2016.08.002. [Epub ahead of print]
Manzoor A1, UlAbdin Z2, Webb BA3, Arif MJ1, Jamil A4.
Venom is a key-factor in the regulation of host physiology by parasitic Hymenoptera and a potentially rich source of novel bioactive substances for biotechnological applications. The limited study of venom from the ectoparasitoid Bracon hebetor, a tiny wasp that attacks larval pest insects of field and stored products and is thus a potential insect control agent, has not described the full complement and composition of these biomolecules. To have a comprehensive picture of genes expressed in the venom glands of B. hebetor, a venom gland transcriptome was assembled by using next generation sequencing technologies followed by de novo assemblies of the 10.81 M sequence reads yielded 22,425 contigs, of which 10,581 had significant BLASTx hits to know genes. The majority of hits were to Diachasma alloeum, an ectoparasitoid from same taxonomic family, as well as other wasps. Gene ontology grouped the sequences into molecular functions in which catalytic activity with 42.2% was maximum, cellular components in which cells with 33.8% and biological processes among which metabolic process with 30% had the most representatives. In this study, we highlight the most abundant sequences, and those that are likely to be functional components of the venom for parasitization. Full length ORFs of Calreticulin, Venom Acid Phosphatase Acph-1 like protein and arginine kinase proteins were isolated and their tissue specific expression was studied by RT-PCR. Our report is the first to characterize components of the B. hebetor venom glands that may be useful for developing control tools for insect pests and other applications.
Copyright © 2016 Elsevier Inc. All rights reserved.
Bracon hebetor; De novo assembly; Illumina technology; Next generation sequencing; RNA-seq; Transcriptome; Venom glands
PMID: 27636656 DOI: 10.1016/j.cbd.2016.08.002
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Genome Biol Evol. 2016 Sep 15. pii: evw229. [Epub ahead of print]
Griffith OW1, Brandley MC2, Belov K3, Thompson MB3.
The evolution of new organs is difficult to study because most vertebrate organs evolved only once, more than 500 million years ago. An ideal model for understanding complex organ evolution is the placenta, a structure that is present in live bearing reptiles and mammals (amniotes), which has evolved independently more than 115 times. Using transcriptomics, we characterised the uterine gene expression patterns through the reproductive cycle of a viviparous skink lizard, Pseudemoia entrecasteauxii Then we compare these patterns with the patterns of gene expression from two oviparous skinks Lampropholis guichenoti and Lerista bougainvillii While thousands of genes are differentially expressed between pregnant and non-pregnant uterine tissue in the viviparous skink, few differentially expressed genes were identified between gravid and non-gravid oviparous skinks. This finding suggests that in P. entrecasteauxii, a pregnant specific gene expression profile has evolved, allowing for the evolution of pregnancy specific innovations in the uterus. We find substantial gene expression differences between the uterus of the chorioallantoic and yolk sac placenta in P. entrecasteauxii, suggesting these placental regions are specialized for different placental functions. In particular, the chorioallantoic placenta is likely a major site of nutrient transport by membrane bound transport proteins, whilst the yolk sac placenta also likely transports nutrients but via apocrine secretions. We discuss how the evolution of transcription factor networks are likely to underpin the evolution of the new transcriptional states in the uterine tissue of viviparous reptiles.
© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Pseudemoia; RNA-seq; convergent evolution; lizard; placenta; viviparity