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Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

机译：日本朱I的全基因组SNP和STR发现以及日本人口创始人之间的遗传多样性

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摘要

The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management. To discover genome-wide single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) while obtaining genotype data of these polymorphic markers in each founder, reduced representation libraries were independently prepared from each of the founder genomes and sequenced on an Illumina HiSeq2000. This yielded 316 million 101-bp reads. Consensus sequences were created by clustering sequence reads, and then sequence reads from each founder were mapped to the consensus sequences, resulting in the detection of 52,512 putative SNPs and 162 putative STRs. The numbers of haplotypes and STR alleles and the investigation of genetic similarities suggested that the total genetic diversity between the founders was lower, although we could not identify a pair with closely related genome sequences. This study provided important insight into protocols for genetic management of the captive breeding population of Japanese crested ibis in Japan and towards the national project for reintroduction of captive-bred individuals into the wild. We proposed a simple, efficient, and cost-effective approach for simultaneous detection of genome-wide polymorphic markers and their genotypes for species currently lacking a reference genome sequence.
机译：日本凤头宜必思酒店是国际保存的，濒危物种。在日本，已经建立了圈养繁殖计划来保护该物种。由于目前的日本朱i种群仅来自中国政府捐赠的5位创始人，因此了解它们之间的遗传多样性对于有效的种群管理至关重要。为了发现全基因组范围内的单核苷酸多态性（SNP）和短串联重复序列（STR），同时获得每个创建者中这些多态性标记的基因型数据，从每个创建者基因组中独立制备了简化的表征文库，并在Illumina HiSeq2000上进行了测序。这产生了3.16亿个101 bp的读取。通过聚类序列读取创建共识序列，然后将来自每个创建者的序列读取映射到共识序列，从而检测到52,512个推定的SNP和162个推定的STR。单倍型和STR等位基因的数量以及对遗传相似性的研究表明，尽管我们无法鉴定出一对具有密切相关的基因组序列的对，但创始人之间的总遗传多样性较低。这项研究为在日本对日本朱i人工繁殖的种群进行遗传管理的方案，以及为将人工繁殖的个体重新引入野外的国家计划提供了重要的见识。我们提出了一种简单，有效且具有成本效益的方法，用于同时检测当前缺少参考基因组序列的物种的全基因组多态性标记及其基因型。

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