• Energy Research

Abstract The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change.

The White-flippered penguin is a small penguin closely related to the New Zealand little blue penguin. It is occasionally considered a unique species or sometimes a subspecies of the New Zealand little blue penguin, however genetic research indicates that the two taxa are probably incipient. The reason it is occasionally considered a separate species or subspecies is because it has white markings on its flippers. Most taxonomists consider it to be a colour morph of the New Zealand little blue penguin. It nests in headlands, caves, rock jumbles and in the sheltered areas at the bases of bays, only on Banks Peninsula and Motunau Island near Christchurch, New Zealand. The white-flippered penguin is a Taonga, or treasured possession in Mori culture. The International Union for Conservation of Nature (IUCN) considers all Eudyptula penguins as least concern.We sequenced the genome of an adult White-flippered penguin from Christchurch Antarctic Centre, originally from Banks Peninsula, Canterbury, New Zealand South Island (provided by Pauline Howard) to a depth of approximately 100x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.3Gb, with the contig and scaffold N50 values of 93.53Kb and 20.85Mb respectively. We identified 17424 protein-coding genes.

The Yellow-eyed penguin (hoiho in Mori) is native to New Zealand. It breeds along the eastern and south-eastern coasts of the New Zealand South Island, Stewart Island, Auckland Islands and Campbell Islands. They are a popular tourist venue in Otago. On the New Zealand mainland, the Yellow-eyed penguin has declined significantly - attributed to a range of factors including climate change and fisheries. Local extinction on the mainland is possible in the next 20 to 40 years. They are larger in size, but very closely related to the recently extinct Waitaha penguin and Chatham Island Yellow-eyed penguin. Genetic work demonstrates that the Yellow-eyed penguin expanded its range from the sub-Antarctic islands to the main islands of New Zealand after the extinction of the Waitaha penguin. The Yellow-eyed penguin is classified as endangered by the International Union for Conservation of Nature (IUCN) and is considered one of the world's rarest penguin species. The Yellow-eyed penguin is a Taonga, or treasured possession in Mori culture.We sequenced the genome of an adult Yellow-eyed penguin from Otago Peninsula, New Zealand South Island (provided by Melanie Young) to a depth of approximately 88x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.25Gb, with the contig and scaffold N50 values of 81.99Kb and 22.24Mb respectively. We identified 16563 protein-coding genes.

The Eastern rockhopper penguin is a small crested penguin. It is closely related to the Western rockhopper penguin, however there is still some debate about whether both are considered incipient species, sub-species or distinct species. Recent genetic work suggests they are probably separate species. The Eastern rockhopper penguin breeds widely on subantarctic islands from New Zealand Campbell/Auckland/Antipodes Islands to the Prince Edward Islands group. The International Union for Conservation of Nature (IUCN) classifies the Southern rockhopper penguin group (including both the Eastern and the Western rockhopper penguin) as vulnerable.We sequenced the genome of an adult Eastern rockhopper penguin from Possession Island, Crozet Islands (provided by Yves Cherel) to a depth of approximately 163x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.25Gb, with the contig and scaffold N50 values of 72.54Kb and 6.13Mb respectively. We identified 15963 protein-coding genes.

The Western rockhopper penguin (also known as the Southern rockhopper penguin or American Southern rockhopper penguin) is a small crested penguin. It is closely related to the Eastern rockhopper penguin, and there is still some debate about whether both are considered incipient species, sub-species or distinct species. Recent genetic work suggests they are probably separate species. The Western rockhopper penguin breeds on subantarctic islands of the western Pacific and Indian Oceans, as well as around the southern coasts of South America. The International Union for Conservation of Nature (IUCN) classifies the Southern rockhopper penguin group (including both the Western and the Eastern rockhopper penguin) as vulnerable.We sequenced the genome of an adult Western rockhopper penguin from Falkland Islands/Malvinas (provided by Dee Boersma) to a depth of approximately 162x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.26Gb, with the contig and scaffold N50 values of 64.46Kb and 1.86Mb respectively. We identified 16280 protein-coding genes.

The New Zealand little blue penguin (also known as fairy penguin, blue penguin, little penguin and koror in Mori) is one of the smallest penguins. It is found on the coastlines of New Zealand and the Chatham Islands. They have a slate-blue plumage. Recent genetic, morphological and behavioral research has demonstrated that the New Zealand little blue penguin is a seperate species to the Australian fairy penguin, however this still remains controversial. Populations have recently declined, and they are considered as Least Concern by the International Union for Conservation of Nature (IUCN), however this assessment still classifies the Australian and New Zealand species as conspecific. The New Zealand little penguin is a Taonga, or treasured possession in Mori culture.We sequenced the genome of an adult Little blue penguin from National Aquarium of New Zealand, New Zealand North Island (provided by Helen Taylor) to a depth of approximately 87x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.3Gb, with the contig and scaffold N50 values of 86.12Kb and 20.15Mb respectively. We identified 17802 protein-coding genes.

The Snares crested penguin (also known as Snares penguin, Snares Islands penguin, and in Mori it is known as pokotiwha) is endemic only to the New Zealand Snares Islands and Western Chain. It is a crested penguin closely related to the Fiordland crested penguin. Historically, Snares crested and Fiordland crested penguins were considered incipient - however the Snares crested penguin can be distinguished from the Fiordland crested penguin by having bare skin around the base of its bill. The Snares crested penguin breeds among tree roots and rocks in dense forest or in the open, laying two eggs, the second of which is larger and hatches first rather than being the smallest and last to hatch. The International Union for Conservation of Nature (IUCN) classifies the Snares crested penguin as vulnerable. The Snares crested penguin is a Taonga, or treasured possession in Mori culture.We sequenced the genome of an adult Snares-crested penguin from Dunedin Wildlife Hospital, originally from The Snares, New Zealand sub-Antarctic (provided by David Thompson) to a depth of approximately 138x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 29.02Kb and 0.35Mb respectively. We identified 17126 protein-coding genes.

The Galápagos penguin is endemic to the Galápagos Islands, and is the only penguin with breeding colonies north of the equator. The cool waters of the Humboldt and Cromwell Currents allow the species to survive in the tropics, and they have evolved unique adaptations to survive in a tropical environment. The International Union for Conservation of Nature (IUCN) classifies them as endangered.We sequenced the genome of an adult Galápagos penguin from Galápagos Islands (provided by Patricia Parker) to a depth of approximately 87x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.35Gb, with the contig and scaffold N50 values of 70.85Kb and 0.36Mb respectively. We identified 16390 protein-coding genes.