Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator

Abstract

Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted.

Chinese alligator genome illustrates molecular adaptations

“…Phenotypic novelty and diversity may be driven by changes in gene regulation, but changes in the sequence and function of protein-coding genes or expansion and contraction of multi-gene families may also contribute. Wan et al [1] found multiple examples of protein adaptation and gene family expansions that were a key source of phenotypic novelty, supporting the latter view.…”

Conservation Genetics and Genomics of Amphibians and Reptiles

“…Bold new initiatives, among them the Genome 10K Project, that seek to enable the sequencing of 10,000 vertebrate genomes (158) are rapidly closing the genome gap. Reptiles have enjoyed far greater success than amphibians in terms of reasonably high-quality genome assemblies, and as of this writing, four turtles (159,160), four crocodilians (161,162), four squamates (163)(164)(165)(166), and one amphibian (167) have been released and are available to the community. The second is the analysis pipeline, particularly for low-coverage genomic data.…”

Analysis of the reptile CD1 genes: evolutionary implications

“…AlsiCD1.2 is found in scaffold 1413_1 (GenBank accession No: NW_005843837.1), and there are no other genes predicted in this scaffold. The third Chinese alligator CD1 gene (AlsiCD1.3, GenBank accession No: XP_006036211) is found in scaffold 113_1 (GenBank accession No: NW_005842918.1), which contains similar genes to those located on human MHC paralogous chromosome 19 (Wan et al 2013). Fig.…”