Correa Jose Salome, Noble Luke M, Sloat Solomon A, Nguyen Tuc H M, Rockman Matthew V
Department of Biology and Center for Genomics & Systems Biology, New York University, New York, New York.
EnviroDNA, Melbourne, Australia.
bioRxiv. 2025 May 15:2025.05.09.653148. doi: 10.1101/2025.05.09.653148.
nematodes represent a promising model clade for evolutionary genetics and genomics, but research has focused on the three androdioecious species, those with self-fertile hermaphrodites, all in the Elegans Group of species. The majority of species are gonochorists, with males and females, characterized by inconveniently high heterozygosity and inbreeding depression. We have identified , a Japonica Group species from Panamá, as an experimentally tractable gonochorist. We describe a new chromosomal genome assembly of a healthy inbred reference strain, integrating data from PacBio HiFi reads, Illumina short reads, genetic linkage, and HiC chromatin contacts, and experimental gene annotation with short- and long-read data. Several genetic properties that are well characterized in the Elegans Group are present in this Japonica Group species: the organization of the genetic map, cosegregation of autosomal indels and sex chromosomes, and segregation distortion due to elements, demonstrated here for the first time in a gonochoristic species. Some aspects of the genome are highly conserved, including synteny across the six chromosomes and the distributions of repetitive sequences and genes along each chromosome. Other features are quite distinctive, including evolved shifts in GC composition & heterogeneity along the genome. Both codon & amino acid usage are shifted in concert with the species' genomic GC content. has an unusually large X chromosome, which we find is associated with multiple local gene family expansions. These findings and resources lay the foundation for further experimental and computational studies of genetics and genomics.
线虫是进化遗传学和基因组学中一个很有前景的模型分支，但研究主要集中在三种雄雄同体物种上，即那些具有自交可育雌雄同体的物种，它们都属于秀丽隐杆线虫物种群。大多数物种是雌雄异体的，有雄性和雌性，其特点是杂合度高得不便研究且存在近交衰退。我们已经确定了一种来自巴拿马的粳稻组物种，它是一种实验上易于处理的雌雄异体物种。我们描述了一个健康近交参考品系的新染色体基因组组装，整合了来自PacBio HiFi reads、Illumina短读长、遗传连锁和HiC染色质接触的数据，以及基于短读长和长读长数据的实验性基因注释。在秀丽隐杆线虫物种群中得到充分表征的几个遗传特性也存在于这个粳稻组物种中：遗传图谱的组织、常染色体插入缺失与性染色体的共分离，以及由于某些元件导致的分离畸变，这在雌雄异体的线虫物种中是首次得到证明。基因组的一些方面高度保守，包括六条染色体间的共线性以及每条染色体上重复序列和基因的分布。其他特征则相当独特，包括基因组中GC组成和异质性的进化变化。密码子和氨基酸的使用都与物种的基因组GC含量协同变化。该物种有一条异常大的X染色体，我们发现它与多个局部基因家族的扩张有关。这些发现和资源为进一步对线虫遗传学和基因组学进行实验和计算研究奠定了基础。
