Looking at Alala Genomes

We are studying the mitogenomes of the highly endangered Hawaiian crow or alala.

We are studying the mitogenomes of the highly endangered Hawaiian crow or alala.

The capability of reading entire genomes of threatened and endangered species provides a wonderful opportunity to understand how to save them from the brink of extinction. The genomic era has opened up exciting possibilities in the field of conservation biology by enabling more robust studies on species’ genetic variation, population structure, and the identification of genes associated with low reproductive success or disease susceptibility. Genomics data have also assisted in identifying cryptic species in the wild, revisiting species classification, and proposing new units of conservation.

In every vertebrate cell two kinds of genomes are found. One is located in the cell’s nucleus and contains the genetic make up of both paternal and maternal progenitors. This genome generally is huge in size, representing about 20,000 to 30,000 genes that are responsible for physical traits. The second and much smaller genome is found in the mitochondria, structures that produce the chemical energy required by the cell. The complete mitochondrial DNA (mtDNA) genome or mitogenome is composed of only 37 genes inherited solely from the mother and allows one to trace the evolutionary history of maternal lineages in a population.

In the Genetics Lab at the San Diego Zoo Institute for Conservation Research, we have recently started to study the mitogenomes of the highly endangered Hawaiian crow or alala, an endemic species to the Hawaiian island that is extinct in the wild. Only a small population of 109 individuals remains at the Keauhou and Maui bird conservation centers, operated by San Diego Zoo Global. Examining alala mitogenomes will help assess the evolutionary potential of this species to survive and respond to environmental changes and diseases, in addition to assisting with its management in captivity by identifying valuable individuals or genetic lineages for breeding.

Our Genetics Lab uses the next-generation sequencing technologies of the Ion Torrent, donated by Life Technologies.

Our Genetics Lab uses the next-generation sequencing technologies of the Ion Torrent, donated by Life Technologies.

The mitogenome project began with the extraction of total DNA from alala blood, tissue, and cell lines available at the Institute’s Frozen Zoo® from 10 founders of the current captive population: 6 females and 4 males. The mtDNA was captured from total DNA and tagged with unique barcode sequences for each individual. All mtDNAs were pooled and loaded on a sequencing chip and then sequenced in the Genetics Lab using next-generation sequencing technologies of the Ion Torrent, donated by Life Technologies. Thousands of genomic reads representing single mitogenomes were assembled and compared among founders to identify genetic variants.

Not unexpectedly, low genetic variation was found in the alala founders. Within the ten genomes, only two were distinct, with ten genetic variants located on eight different genes. However, this new approach did detect maternal genetic variation previously unnoticed by single gene procedures, supporting the importance of screening genome-wide genetic variation in threatened and endangered species with small population sizes and subject to inbreeding. The possibility to apply the “mitogenomic approach” to species of concern such as gorillas and rhinos represents an exciting opportunity for the Genetics Division to incorporate cutting-edge procedures in assisting with the management of wild and captive species. This more complete source of genetic information may become a crucial tool for species recovery and ensuring success of captive breeding programs.

Cynthia Steiner, Ph.D., is a senior research associate with the San Diego Zoo Institute for Conservation Research. Read her previous post, Revealing the Secrets of Sloths.

2 Responses to Looking at Alala Genomes

  1. Dear Dr Steiner, I am a PhD student at the Monash University in Malaysia. My research is on genetics of invasive crow species, Corvus splendens. One of the aims is to look closely at the full mitochondrial genome of birds from different geographical locations to search for signatures of positive and purifying selection. It would be extremely interesting to compare full mitogenome of this invasive species against mitogenome of endangered Hawaiian crow. May I know if you have actually published the genome yet? Could not find it in GenBank; is it available yet?
    Thanking you. Urszula

  2. Dear Urszula, thank you for your interest in our work. Results from this mitogenomic study on alala will be soon published and available in Genbank for downloading. I hope this information will serve your research on other Corvidae species. All the best, Cynthia

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