Summary The Indo-Pacific humpback dolphin ( Sousa chinensis ) is a small inshore species of odontocete cetacean listed as Vulnerable on the IUCN Red List. Here, we report on the evolution of S . chinensis chromosomes from its cetruminant ancestor and elucidate the evolutionary history and population genetics of two neighboring S . chinensis populations. We found that breakpoints in ancestral chromosomes leading to S . chinensis could have affected the function of genes related to kidney filtration, body development, and immunity. Resequencing of individuals from two neighboring populations in the northwestern South China Sea, Leizhou Bay and Sanniang Bay, revealed genetic differentiation, low diversity, and small contemporary effective population sizes. Demographic analyses showed a marked decrease in the population size of the two investigated populations over the last ~4,000 years, possibly related to climatic oscillations. This study implies a high risk of extinction and strong conservation requirement for the Indo-Pacific humpback dolphin.

With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG-Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge.This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications.

19Domestic ducks are considered to have been tamed from the mallard or a descendant 20 of the mallard and the spot-billed duck. Domestic ducks show remarkable phenotypic 21 variation in morphology, physiology and behaviour. However, the molecular genetics 22 of the origin and phenotypic variation of ducks are still poorly studied. 23 Here, we present mallard and spot-billed genomes and perform whole-genome 24 sequencing on eight domestic duck breeds and eight wild duck species. Surprisingly, 25 analyses of these data support a model in which domestic ducks diverged from their 26 closest wild lineage (mallard ducks and spot-billed ducks) at the last glacial period 27 (LGP, 100-300 kilo years ago (Kyr)). The wild lineage further speciated into mallard 28 ducks and spot-billed ducks approximately 70 Kyr, whereas the domestic lineage 29 population decreased through the LGP. A scan of wild duck genomes compared with 30 domestic duck genomes identified numerous loci that may have been affected by 31 positive selection in ancestral wild ducks after their divergence from domestic 32 lineages. Function analyses suggested that genes usually affecting organ development 33 and energy metabolism may involve long-distance flight ability. Further selective 34 sweep analyses identified two genes associated with egg production and three genes 35 related to feeding modulation under selection in domestic ducks. These analyses 36 unravel a distinct evolutionary pattern of ducks and two wild duck de novo genomes, 37 thus providing a novel resource for speciation studies.38 40 41 65 zonorhyncha, refer as spot-billed)(Steve, 1992). Those are mainly based on their 66 similar outlooks, habits, and distributions. Moreover, there are broad phenotypic 67 4 differences between domestic ducks and their wild relatives, such as loss of flight and 68 migration ability, reduced brain size, and increased body size and fertility. Although 69 researches of steamer ducks on flightless and genetic association with selected traits 70 on domestic ducks have been performed (Zhang et al., 2018; Zhou et al., 2018). They 71 revealed diverse mechanisms from others and It indicating a historical context would 72 be important in understanding functional changes and its ecology factors (Burga et al., 73 2017; Campagna, McCracken, & Lovette, 2019). However, the demographic 74 inference suffered from lacking of solid history information, too many possibilities, 75 complex history and no robust mutation rates. The historical relationships of ducks, 76 like many other domestic animals, are still unclear (Albarella, 2005; Larson & Fuller, Despite, lots of efforts have committed and traditional domestication hypotheses have 79 been found incompatible with genetic data, and the direct ancestors of domesticated 80 animals are still unclear (Frantz et al., 2015; Freedman et al., 2014). Nevertheless, 81 some genetic analyses were still conducted under the pre-assumption of some 82 untested recoding and questionable hypothesis (Irving-Pease, Frantz, Sykes, Callou, 83 &...

Background Primary hyperoxaluria(PH)is a rare autosomal recessive genetic disease that contains three subtypes (PH1, PH2 and PH3). Approximately 80% of PH patients has been reported as subtype PH1, this subtype of PH has been related to a higher risk of renal failure at any age. Several genetic studies indicate that the variants in gene AGXT are responsible for the occurrence of PH1. However, the population heterogeneity of the variants in AGXT makes the genetic diagnosis of PH1 more challenging as it is hard to locate each specific variant. It is valuable to have a complete spectrum of AGXT variants from different population for early diagnosis and clinical treatments of PH1. Case presentation In this study, We performed high-throughput sequencing and genetic analysis of a 6-year-old male PH1 patient from a Chinese family. Two variants (c.346G > A: p.Gly116Arg; c.864G > A: p.Trp288X) of the gene AGXT were identified. We found a nonsense variant (c.864G > A: p.Trp288X) that comes from the proband’s mother and has never been reported previously. The other missense variant (c.346G > A: p.Gly116Arg) was inherited from his father and has been found previously in a domain of aminotransferase, which plays an important role in the function of AGT protein. Furthermore, we searched 110 pathogenic variants of AGXT that have been reported worldwide in healthy local Chinese population, none of these pathogenic variants was detected in the local genomes. Conclusions Our research provides an important diagnosis basis for PH1 on the genetic level by updating the genotype of PH1 and also develops a better understanding of the variants in AGXT by broadening the variation database of AGXT according to the Chinese reference genome.

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