Elephant transcriptome provides insights into the evolution of eutherian placentation

Abstract

The chorioallantoic placenta connects mother and fetus in eutherian pregnancies. In order to understand the evolution of the placenta and provide further understanding of placenta biology, we sequenced the transcriptome of a term placenta of an African elephant (Loxodonta africana) and compared these data with RNA sequence and microarray data from other eutherian placentas including human, mouse, and cow. We characterized the composition of 55,910 expressed sequence tag (i.e., cDNA) contigs using our custom annotation pipeline. A Markov algorithm was used to cluster orthologs of human, mouse, cow, and elephant placenta transcripts. We found 2,963 genes are commonly expressed in the placentas of these eutherian mammals. Gene ontology categories previously suggested to be important for placenta function (e.g., estrogen receptor signaling pathway, cell motion and migration, and adherens junctions) were significantly enriched in these eutherian placenta-expressed genes. Genes duplicated in different lineages and also specifically expressed in the placenta contribute to the great diversity observed in mammalian placenta anatomy. We identified 1,365 human lineage-specific, 1,235 mouse lineage-specific, 436 cow lineage-specific, and 904 elephant-specific placenta-expressed (PE) genes. The most enriched clusters of human-specific PE genes are signal/glycoprotein and immunoglobulin, and humans possess a deeply invasive human hemochorial placenta that comes into direct contact with maternal immune cells. Inference of phylogenetically conserved and derived transcripts demonstrates the power of comparative transcriptomics to trace placenta evolution and variation across mammals and identified candidate genes that may be important in the normal function of the human placenta, and their dysfunction may be related to human pregnancy complications.

FIG. 1.—

Contig length distribution and composition. Summary of cDNA contig length distribution and composition in this study. (A) Distribution of assembled contig length; (B) pie chart depicts the results of BLAT searches using the 55,910 transcribed elephant contigs as the subject for queries to mammalian genomic, cDNA, ncRNA, and microbial databases. Known transcripts (red) are those elephant contigs that have sequence similarity to sequences in human and/or mouse and/or cow Ensembl cDNA gene databases. Purple indicates elephant transcripts that share a similarity to noncoding RNA sequences (see Materials and Methods for database details). Blue indicates those elephant transcripts that have significant similarity to only the Ensembl elephant genomic database. Green indicates those transcripts that did not return hits for any of our BLAT queries. A small percentage of transcripts shared sequence similarity only with bacterial sequence (light blue).

FIG. 2.—

Elephant novel transcripts and new exons. Novel elephant transcripts were discovered using our analyses pipeline (supplementary fig. S1, Supplementary Material online). The University of California–Santa Cruz (UCSC) BLAT was used to align contigs to elephant genome data. Direction of transcription was determined by UCSC BLAT results. Novel elephant transcripts were classified into two groups: (A) Novel elephant transcripts that are not adjacent to any known transcribed regions. (B) Novel elephant transcripts that are in Ensembl transcript intron regions.

FIG. 3.—

Phylogeny. Tree topology and divergence dates used for this study were derived from Murphy et al. (2007) and Wildman et al. (2007). The human, mouse, cow, opossum, platypus, and chicken sequence data are considered high-quality genomic and/or transcriptome data. Atla, Atlantogenata; Euarcho, Euarchontoglires; Laur, Laurasiatheria; Afro, Afrotheria.

FIG. 4.—

Eutheria placenta shared and lineage-specific expressed genes. Genomic data from seven species (human, mouse, cow, elephant, opossum, platypus, and chicken) were used in our comparative genomics study. Human, mouse, and cow PE genes were obtained from publically available data (see Materials and Methods). Elephant PE genes were generated in this study. Numbers on each branch represent the branch (i.e., lineage specific) PE genes as determined by the Markov-clustering algorithms and our custom quality control procedure (see Materials and Methods).