Polashock James, Zelzion Ehud, Fajardo Diego, Zalapa Juan, Georgi Laura, Bhattacharya Debashish, Vorsa Nicholi
USDA, Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Lab, 125A Lake Oswego Rd,, Chatsworth, New Jersey 08019, USA.
BMC Plant Biol. 2014 Jun 13;14:165. doi: 10.1186/1471-2229-14-165.
The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.
The genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).
Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.
美国蔓越莓（Vaccinium macrocarpon Ait.）是仅有的三种原产于北美的广泛种植的水果作物之一，另外两种是蓝莓（Vaccinium spp.）和本土葡萄（Vitis spp.）。在分类学上，蔓越莓属于核心杜鹃花目，目前该目缺乏基因组序列数据。此外，蔓越莓能产生许多重要的多酚类次生化合物，其中一些对人体健康有益。虽然新一代测序技术推动了全基因组测序的发展，但从复杂二倍体（及更高倍体）生物的短读长序列数据成功组装基因组的一个主要障碍是杂合性。蔓越莓具有二倍体（2n = 2x = 24）且自花可育的优势。为尽量减少杂合性问题，我们对源自品种Ben Lear连续五代自交的第五代近交基因型（F≥0.97）的基因组进行了测序。
大果越橘的基因组大小估计约为470 Mb。基因组序列被组装成229,745个支架，代表420 Mbp（N50 = 4,237 bp），平均覆盖度为20X。预测基因数量为36,364个，占组装基因组的17.7%。在预测基因中，30,090个基于同源性被归为候选基因。转录组数据支持的基因共有13,170个（36%）。
蔓越莓基因组的鸟枪法测序，平均测序覆盖度为20X，实现了高效组装和基因识别。鉴定出的候选基因是进一步研究重要生化途径和细胞过程以及用于育种标记开发和园艺特性（如抗病性）研究的有用资源。
