Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome.
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome.
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DOI：
10.1186/s12864-020-07027-6
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发表时间：
2020-10-15
期刊：
影响因子：
4.4
通讯作者：
Hui JHL
中科院分区：
文献类型：
--
作者：
Li Y;Nong W;Baril T;Yip HY;Swale T;Hayward A;Ferrier DEK;Hui JHL
含有同源盒的基因编码参与动物、植物和真菌发育的关键转录因子，同源盒基因的变化与新的身体结构和形态的进化有关。在动物中，一些同源框基因在基因组中聚集在一起，要么是祖先基因组排列的残余物，要么是由于协调的基因调控。因此，对跨动物系统发育的同源框基因组织的分析为基因组组织和发育基因控制的进化及其相互作用提供了重要的见解。然而，几个关键动物祖先的同源框基因组织仍有待充分阐明，包括软体动物、轮轮动物和两侧对称动物。在这里，我们展示了香港牡蛎 Magallana hongkongensis (2n = 20) 的高质量染色体水平基因组组装，其中 93.2% 的基因组序列包含在 10 个假分子上 (~ 758 Mb，支架 N50 = 72.3 Mb)。我们的基因组组装是使用 Hi-C 读段构建的，与 Peng 等人最近发表的 M. hongkongensis 基因组相比，有利于更大的支架尺寸。 （Mol Ecol Resources，2020），使用 Crassostrea gigas 组件搭建脚手架。我们的基因组中总共纳入了 46,963 个预测基因模型（45,308 个蛋白质编码基因），BUSCO 估计的基因组完整性为 94.6%。相对于其他软体动物谱系的可用数据，对同源盒基因连锁进行了详细分析。本研究中进行的分析以及随附的基因组序列为这种具有经济和文化价值的牡蛎物种提供了重要的遗传资源，并为更广泛地提高对动物生物学和进化的理解提供了平台。转座元素含量与其他软体动物物种中发现的含量相当，这与最近另一项分析的结论相反。此外，我们的染色体水平组装允许推断含有同源盒的基因的古代基因连锁（同线性），尽管许多同源盒基因簇（如 Hox/ParaHox 簇）正在软体动物（如牡蛎）中分散。
Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
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影响因子：
16.6
作者：
Adema CM;Hillier LW;Jones CS;Loker ES;Knight M;Minx P;Oliveira G;Raghavan N;Shedlock A;do Amaral LR;Arican-Goktas HD;Assis JG;Baba EH;Baron OL;Bayne CJ;Bickham-Wright U;Biggar KK;Blouin M;Bonning BC;Botka C;Bridger JM;Buckley KM;Buddenborg SK;Lima Caldeira R;Carleton J;Carvalho OS;Castillo MG;Chalmers IW;Christensens M;Clifton S;Cosseau C;Coustau C;Cripps RM;Cuesta-Astroz Y;Cummins SF;di Stephano L;Dinguirard N;Duval D;Emrich S;Feschotte C;Feyereisen R;FitzGerald P;Fronick C;Fulton L;Galinier R;Gava SG;Geusz M;Geyer KK;Giraldo-Calderón GI;de Souza Gomes M;Gordy MA;Gourbal B;Grunau C;Hanington PC;Hoffmann KF;Hughes D;Humphries J;Jackson DJ;Jannotti-Passos LK;de Jesus Jeremias W;Jobling S;Kamel B;Kapusta A;Kaur S;Koene JM;Kohn AB;Lawson D;Lawton SP;Liang D;Limpanont Y;Liu S;Lockyer AE;Lovato TL;Ludolf F;Magrini V;McManus DP;Medina M;Misra M;Mitta G;Mkoji GM;Montague MJ;Montelongo C;Moroz LL;Munoz-Torres MC;Niazi U;Noble LR;Oliveira FS;Pais FS;Papenfuss AT;Peace R;Pena JJ;Pila EA;Quelais T;Raney BJ;Rast JP;Rollinson D;Rosse IC;Rotgans B;Routledge EJ;Ryan KM;Scholte LLS;Storey KB;Swain M;Tennessen JA;Tomlinson C;Trujillo DL;Volpi EV;Walker AJ;Wang T;Wannaporn I;Warren WC;Wu XJ;Yoshino TP;Yusuf M;Zhang SM;Zhao M;Wilson RK
通讯作者：
Wilson RK
影响因子：
3.3
作者：
Barton-Owen TB;Szabó R;Somorjai IML;Ferrier DEK
通讯作者：
Ferrier DEK
影响因子：
2.9
作者：
Castro, LFC;Hoiianda, PWH
通讯作者：
Hoiianda, PWH
影响因子：
9.2
作者：
Du, Xiaodong;Fan, Guangyi;Liu, Xin
通讯作者：
Liu, Xin
影响因子：
3.7
作者：
Gan, Han Ming;Tan, Mun Hua;Miller, Adam D.
通讯作者：
Miller, Adam D.