Mutli-omics data consortium of the brachiopod Lingula anatina. Lingula anatina

This project aims at reporting a chromosome level genome assembly of the brachiopod Lingula anatina by re-sequencing the genome using long read sequencing and Hi-C results to direct genome assembling.The project has two main theme and one sub-theme.Main theme 1: Lingula genome resequencingObjectives:1. Comparing the new chromosome level genome assembly with the previously published Illumina short read sequencing based genome assembly of L. anatina (Luo et al. 2014);2. To explore marcosynteny among the Lophoarata genomes;3. To explore and compare the genomic arrangement of HOX cluster among the Lophoarata.Main theme 2: shell proteomeObjectives:1. To profile L. anatina shell proteome as a representative for the Brachiopoda;2. To profile L. anatina mantle transcriptome and identify mantle specific genes;3. To identify shell matrix proteins (SMPs) and resolve any of those that have low complexity repeat region by IsoSeq data;4. To identify upstream regulatory regions of of SMPs, in order to prepare for future knockout experiments;5. To compare L. anatina shell matrix proteins and their regulatory elements with those from marine calcifiers, including but not restrict to, barnacles, mollusks, bryozoans.Sub-theme: mitogenome re-sequencingObjectives:1. determine the presence of absence of potential functional gene section in the mitogenome based on long read sequencing technique2. validate the presence of the predicted functional gene by Hiseq transrcriptome data

本项目旨在通过长读长测序（long read sequencing）技术对腕足动物鸭嘴舌形贝（Lingula anatina）进行基因组重测序，并结合Hi-C（Hi-C）辅助组装，报道其染色体级基因组组装结果。本项目包含两个核心主题与一个子主题。
主主题1：舌形贝基因组重测序
研究目标：
1. 将本次获得的染色体级基因组组装结果，与此前基于Illumina短读长测序发布的鸭嘴舌形贝基因组组装结果（Luo et al. 2014）进行比较分析；
2. 探讨Lophoarata类群基因组的宏观共线性（macro-synteny）；
3. 分析并比较Lophoarata类群中HOX基因簇（HOX cluster）的基因组排布情况。
主主题2：贝壳蛋白质组（shell proteome）
研究目标：
1. 以鸭嘴舌形贝为腕足动物代表，解析其贝壳蛋白质组特征；
2. 构建鸭嘴舌形贝外套膜转录组图谱，鉴定外套膜特异性表达基因；
3. 鉴定贝壳基质蛋白（shell matrix proteins, SMPs），并借助IsoSeq测序数据解析其中含有低复杂度重复区域的蛋白序列；
4. 鉴定贝壳基质蛋白的上游调控区域，为后续基因敲除实验奠定基础；
5. 将鸭嘴舌形贝的贝壳基质蛋白及其调控元件，与海洋钙化生物（包括但不限于藤壶、软体动物、苔藓虫）的同类物质进行比较分析。
子主题：线粒体基因组重测序（mitogenome re-sequencing）
研究目标：
1. 基于长读长测序技术，确定线粒体基因组中潜在功能基因区段的存在与否；
2. 利用HiSeq转录组测序数据验证预测的功能性基因的表达情况。