Jack of all trades: genome assembly of Wild Jack and comparative genomics of Artocarpus

This dataset comprises all the annotation sequences, figures and other relevant data incorporated in the manuscript. Abstract: Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called "Wild jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species, had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild jack.

本数据集包含该手稿中收录的全部注释序列、图表及其他相关数据。摘要：波罗蜜属（Artocarpus）隶属于桑科（Moraceae），因其种类丰富且富含营养的果实而被称为面包果类植物，其优质木材、药用价值与经济重要性广受赞誉。面包果原产于东南亚地区，目前已被引种至全球各大洲。当前广泛栽培的波罗蜜属物种为波罗蜜（Artocarpus heterophyllus，即Jackfruit）和面包果（Artocarpus altilis，即Breadfruit）。糙叶波罗蜜（Artocarpus hirsutus，又称“野波罗蜜”或“Ayani”）是一种分布于印度西高止山脉的罕见特有森林物种，该物种植株体型更大，所结果实虽体积更小，但营养价值与栽培种相当。本研究对采自印度库格县圣林的糙叶波罗蜜样本进行了全基因组测序与组装。为解析其种群历史与演化历程，我们将野波罗蜜的基因组与已发表的波罗蜜及面包果基因组进行了比较分析。种群历史重建结果表明，相较于系统发育关系，生境因素对这些植物的种群历史影响更为显著。重复基因组区域（尤其是长末端重复序列Copia型转座子（LTR Copia））对波罗蜜的种群动态轨迹产生了强烈影响。进一步研究发现，波罗蜜中近期发生了谱系特异性的LTR Copia扩增，这是导致其基因组规模更大的主要原因。波罗蜜属多个物种中，参与淀粉、蔗糖代谢及植物激素信号转导通路的多个基因，均呈现出选择印记与基因家族演化特征。本研究通过纳入野波罗蜜这一特有物种构建比较基因组学分析框架，为相关领域研究提供了重要见解。

搜集汇总

背景与挑战

背景概述

该数据集支持野生杰克（Artocarpus hirsutus）的全基因组组装和比较基因组学研究，包含注释序列、图表和相关数据。它通过比较野生杰克、杰克果和面包果的基因组，揭示了LTR Copia重复序列对基因组大小和人口历史的影响，并识别了代谢与信号通路基因的进化特征。数据集提供了对Artocarpus属植物进化历史的深入洞察，特别关注了印度西高止山脉特有的野生杰克。