Giraffe genome sequence reveals clues to its unique morphology and physiology

Agaba, Morris; Ishengoma, Edson; Miller, Webb; McGrath, Barbara C.; Hudson, Chelsea N.; Reina, Oscar; Ratan, Aakrosh; Burhans, Rico; Chikhi, Rayan; Medvedev, Paul; Praul, Craig A.; Wu-Cavener, Lan; Wood, Brendan Rich; Robertson, Heather; Penfold, Linda M.; Cavener, Douglas R.

doi:10.1038/ncomms11519

Cited by 53 publications

(70 citation statements)

References 66 publications

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“…1A). Aside from PRPH2 and CYP27B1 which had previously been shown to be candidates for adaptive evolution in giraffe (Agaba et al, 2016), no additional candidates of positive selection were identified in the giraffe lineages by the present analysis. Substitution analysis shows that the majority of sites (>80%) are conserved between okapi and closely related cetartiodactyl mammals (Fig.…”

Section: Resultscontrasting

confidence: 48%

“…Variant sites 180 and 233 have Bayes posterior probability of 0.93 and 0.89 respectively. All giraffe’s sequences were found to be identical between NZOO and MA1 (Agaba et al, 2016) verifying that the identified substitutions are not artifacts. (D) The ribbon diagram of giraffe L-opsin highlighting important sequence changes relative to its secondary structure.…”

Section: Resultsmentioning

confidence: 61%

“…Besides PRPH2 and CYP27B1 (Agaba et al, 2016), this study further identifies selection divergence in CRYAA and OPN1LW between giraffe and other ruminants. Observed amino acid changes associated with selection divergence in giraffe’s CRYAA are shared with okapi and in some cases with other ruminant species (Fig.…”

Section: Discussionmentioning

confidence: 59%

“…However, we recently published giraffe genome and detected signatures of adaptation in few of its vision-associated coding genes (Agaba et al, 2016). These genes included Peripherin-2 ( PRPH2 ) and Cytochrome P450 family 27 ( CYP27B1 ).…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

Ishengoma

Agaba

Cavener

2017

PeerJ

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BackgroundThe capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe’s unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood.MethodsThe recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals.ResultsSignatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW. Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.DiscussionBy taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.

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Section: Resultscontrasting

confidence: 48%

Section: Resultsmentioning

confidence: 61%

Section: Discussionmentioning

confidence: 59%

Section: Introductionmentioning

confidence: 99%

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Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

Ishengoma

Agaba

Cavener

2017

PeerJ

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“…In the giraffe, over half of the genes identified as showing multiple signs of adaption are involved in developmental patterning functional pathways. These include unique changes predicted to be functional in homeobox genes consistent with the growth required to produce and support the long giraffe neck[20]. Killer whale ecotypes show positively selected genes associated with cold adaptation and feeding behavior (mammal or fish predation)[21].…”

Section: Genome Analysis Wish Listsmentioning

confidence: 99%

The value of new genome references

Worley

Richards

Rogers

2017

Experimental Cell Research

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Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10–15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology.

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Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania

Lohay

Lee

Wu-Cavener

et al. 2023

Ecology and Evolution

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The Masai giraffe has experienced a population decline from 70,000 to 35,000 in the past three decades and was declared an endangered subspecies by the IUCN in 2019. The remaining number of Masai giraffe are geographically separated by the steep cliffs of the Gregory Rift escarpments (GRE) in Tanzania and Kenya dividing them into two populations, one west and one east of the GRE. The cliffs of the GRE are formidable barriers to east–west dispersal and gene flow and the few remaining natural corridors through the GRE are occupied by human settlements. To assess the impact of the GRE on Masai giraffe gene flow, we examined whole genome sequences of nuclear and mitochondrial DNA (mtDNA) variation in populations located east (Tarangire ecosystem) and west (Serengeti ecosystem) of the GRE in northern Tanzania. Evidence from mtDNA variation, which measures female‐mediated gene flow, suggests that females have not migrated across the GRE between populations in the Serengeti and Tarangire ecosystems in the past ~289,000 years. The analysis of nuclear DNA variation compared to mtDNA DNA variation suggests that male‐mediated gene flow across the GRE has occurred more recently but stopped a few thousand years ago. Our findings show that Masai giraffes are split into two populations and fulfill the criteria for designation as distinct evolutionary significant units (ESUs), which we denote as western Masai giraffe and eastern Masai giraffe. While establishing giraffe dispersal corridors across the GRE is impractical, conservation efforts should be focused on maintaining connectivity among populations within each of these two populations. The importance of these efforts is heightened by our finding that the inbreeding coefficients are high in some of these Masai giraffe populations, which could result in inbreeding depression in the small and fragmented populations.

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Giraffe genome sequence reveals clues to its unique morphology and physiology

Cited by 53 publications

References 66 publications

Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

The value of new genome references

Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania

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