Applications of next generation sequencing in sessile marine invertabrates
Seventy percent of Earth’s surface are oceans and 99% of the Earth’s living space is provided by the oceans. Besides, oceans provide the highest amount of protein for human consumption although it is being “farmed” mostly from wild animals. Domestication of marine life is almost not existent. Domest...
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| Format: | Dataset |
| Language: | English |
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University of Southern California Digital Library (USC.DL)
2018
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| Online Access: | https://dx.doi.org/10.25549/usctheses-c89-54761 https://digitallibrary.usc.edu/asset-management/2A3BF1W4872U |
| Summary: | Seventy percent of Earth’s surface are oceans and 99% of the Earth’s living space is provided by the oceans. Besides, oceans provide the highest amount of protein for human consumption although it is being “farmed” mostly from wild animals. Domestication of marine life is almost not existent. Domestication of wild species improves yield and efficiency of farming. (Turcotte, Araki, Karp, Poveda, & Whitehead, 2017). This is a contrast to land-based agriculture production, which is mainly based of domesticated products. Ocean based farming, also called aquaculture, has great potential to feed the world. More precisely, aquaculture is defined as the breeding, rearing, and harvesting of all types of animals and plants in any type of water environments. Although aquaculture is a very old practice, up until the 1970’s the amount of sea food produced by aquaculture was approximately the same as the amount of sea food produced by wild capture. After the 1990’s, production from wild capture stayed the same, while aquaculture production increased steadily every year up until 2016 (FAO 2018) and is predicted to continue to grow (FAO, 2016). The main reason for this is that we are already harvesting the wild as much as we can and any further harvesting will result in the decay of natural environment, which provides the food. To prevent this, worldwide fisheries management activities are in place. Given that harvesting the wild habitats is not a sustainable way to increase food production, aquaculture is a great solution for this problem. ❧ There are different types of aquaculture, such as finfish aquaculture or shellfish aquaculture. Finfish aquaculture is an effective way of producing a high amount of fish without depleting the natural fisheries but it has many disadvantages compared to farming sessile invertebrates such as shellfish or barnacles. Farming of sessile invertebrates such as mussels, oysters or barnacles has many advantages compared to finfish aquaculture, among which are animal density and feeding requirements. First, these animals naturally occur at high densities in their natural habitat. Having a high animal density is a requirement for any farming practice. Other species, such as fish, need to be confined in a small space, which is very different than their natural habitat (Fraser, Weary, Pajor, & Milligan, 1997). Sessile invertebrates can often be kept at high density on farms, which are in the natural habitat. Secondly, fish require a very high amount of feeding material, which can be a problem both economically and environmentally (Davis, 2015). Sessile invertebrates, such as shellfish or barnacles, are filter feeders and can feed on the available algae and zooplanktons (FAO, 2016). The amount of waste produced by finfish aquaculture like salmon can have serious environmental impact (Hargrave, 2010). ❧ One problem that arises when animals are kept in high densities is the spread of disease. Viral and bacterial infections can easily transmit and kill crops. These types of diseases are manifested based on the interaction between the host and disease agent, which has three components: environment, timing and genetic background. The environmental conditions need to be such that the animal is susceptible and the disease agent is active. Disease agent needs to attack the host in the right time of the year and at the right stage in the host’s development. Beside the genetic background of the host animal is a very crucial factor in the resistance of the host against the disease agent. It has been shown that selective breeding can improve resistance against bacterial and viral infections (Houston & Houston, 2017; Kjøglum, Henryon, Aasmundstad, & Korsgaard, 2008; Yáñez, Houston, & Newman, 2014). One method to tackle this problem is by understanding genetic basis of disease causing agents. In this thesis, the genetic basis of OsHV-1 viral resistance in Pacific oyster, Crassostrea gigas, is investigated. Pacific oyster is a very important sea food and it is one of the most produced shellfish species. This virus attacks oysters early in their development and can cause huge mortalities, up to 100% (Roque et al., 2012; Segarra et al., 2010). This is a major problem in the oyster industry. The second chapter of this thesis is about using a next generation genotyping method, called genotyping-by-sequencing, to dissect the genetic basis for resistance to the OsHV-1 virus. This will allow development of biomarker assisted selection to improve the aquaculture operations. ❧ In the third chapter, the issue of environmental signals that effect the internal clocks will be investigated. To study internal clocks, based on lunar and solar cycles, we focus on the Gooseneck barnacle, Pollicipes polyemerus, which is a rocky intertidal arthropod. This is an extreme habitat with constantly changing environment due to tides. This species is also an important food source with big fisheries in Canada. A sister species (Pollicipes pollicipes), which is morphologically similar to P. polymerus, is the focus of large fisheries in Spain and Portugal. Although this species has the same important properties mentioned above for oysters (animal density and feeding requirements) to be used in aquaculture, there isn’t any successful aquaculture operation for this species. This is mainly because no one has been able to keep P. polymerus alive in an aquaculture setting. We hypothesize that this is mainly due to the peculiar characteristics of the intertidal habitat. P. polymerus is an exclusive species to the intertidal and it is never found sub-tidally. It is always found in the exposed areas with very strong wave action. Those conditions need to be simulated in order to achieve aquaculture activities for this species. This chapter will investigate how barnacles are adapted in this habitat through regulation of their gene expressions. ❧ The fourth chapter is about the investigation of population structure of P. polymerus and generating a de-novo genome assembly for this species. Availability of a genome assembly is crucial to study population genomics or to implement genomics based selection strategies. ❧ All chapters of this thesis utilize NGS (next generation sequencing) to solve problems in ecologically and commercially valuable marine sessile invertebrates. The second chapter tackles the problem of genetic basis of disease resistance. Previous studies investigated the same problem using SNP arrays or microsatellites (Gutierrez et al., 2018; Sauvage et al., 2010; Segarra et al., 2010). With the rapid cost reduction in NGS, there is likely to be a shift to this approach in this field (Park & Kim, 2016). There is no need for the construction of SNP arrays, which can be costly for commercial application, for NGS. Although there is a need for a good quality reference genome to utilize NGS for problems such as understanding the genetic basis of disease resistance. The study organism in the second chapter of this thesis, Crassostrea gigas, already have a decent quality genome (Zhang et al., 2012), but it is still far from being a chromosomal-level genome assembly (Hedgecock et al 2015). Because of this, we constructed a linkage map from our families to be able to position our markers on 10 linkage groups. Although the absence of an accurate genome assembly, is a limitation for our study, as the cost of NGS declines, our approach is likely to be more suitable for commercial application. Besides, being able to perform genomic analysis without relying on pre-constructed SNP arrays allows for detection of previously unknown variants in natural populations. In the third chapter, we are investigating the internal clocks of Pollicipes polymerus, using whole-transcriptome sequencing. Previous studies relied on microarrays for transcriptomic studies (Gracey et al., 2008). These microarrays need to be designed specifically for each study organism. In this chapter, we investigate the whole transcriptome without relying on any previous genomics information. We generated a de-novo transcriptome assembly from the samples and annotated the transcriptome by using public databases. The constructed transcriptome was used to investigate gene expression patterns to understand the internal clock of P. polymerus. The pipeline developed in this chapter can be easily extended to study other non-model animal systems that lacks genomic resources. The fourth chapter investigates the population structure of P. polymerus. Here we use a pooled, whole-genome sequencing approach. As mentioned, there are no genomic resources for this species, so we constructed a de-novo genome assembly and then used pooled, whole-genome sequencing to investigate the population structure along the coast of Southern California. This chapter generated a valuable resource for this species, which is a draft genome assembly. |
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