Biology subjects

Jin, J.-J.

Publications and source records attributed to Jin, J.-J..

3 recordsLinked to original sources

bioRxiv2023

More than a prickly morphology: plastome variation in the prickly pear cacti (Opuntieae)

Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages including gene losses, inversions, boundary movements, or loss of the canonical inverted repeat (IR) region. Here, we further investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent a diverse and important lineage of Cactaceae. We assembled the plastome of 43 species, representing a comprehensive sampling of the tribe including all seven genera. Plastomes varied considerably in length from 121 kbp to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including the lack of the canonical IR in some lineages, and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported deviating in the presence of the IR region or the genes contained in the IR. Plastomes sequences resolved phylogenetic relationships within major clades of Opuntieae but presented some contentious nodes depending on the data set analyzed (e.g., whole plastome vs. genes only). Incongruence analyses revealed that few plastome regions are supporting the most likely topology, while disputing topologies are driven by a handful of plastome markers, which may be the result of hard recalcitrant nodes in the phylogeny or by the lack of phylogenetic signal in certain markers. Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of cactus plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure, and content, and can be important for the recognition of species in some major clades. Unraveling connections between the causes of plastome variation and the consequences on species biology, ecology, diversification, and adaptation, is a promising endeavor.

plant biology↗

bioRxiv2022

Comparative genomics in Orobanchaceae provides insight into the origin and evolution of plant parasitism

Orobanchaceae is the largest family of parasitic plants, containing autotrophic and parasitic plants with all degrees of parasitism. This makes it by far the best family for studying the origin and evolution of plant parasitism. Here we provide three high-quality genomes of orobanchaceous plants, the autotrophic Lindenbergia luchunensis and the holoparasitic plants Phelipanche aegyptiaca and Orobanche cumana. Phylogenomic analysis of these three genomes together with those previously published and the transcriptomes of other orobanchaceous species, created a robust phylogenetic framework for Orobanchaceae. We found that an ancient whole-genome duplication (WGD; about 73.48 Mya), which occurred earlier than the origin of Orobanchaceae, might have contributed to the emergence of parasitism. However, no WGD events occurred in any lineage of orobanchaceous parasites except for Striga after divergence from their autotrophic common ancestor, suggesting that, in contrast to previous speculations, WGD is not associated with the emergence of holoparasitism. We detected evident convergent gene loss in all parasites within Orobanchaceae and between Orobanchaceae and dodder Cuscuta australis. The gene families in the orobanchaceous parasites showed a clear pattern of recent gains and expansions. The expanded gene families are enriched in functions related to the development of the haustorium, suggesting that recent gene family expansions may have facilitated the adaptation of orobanchaceous parasites to different hosts. This study illustrates a stepwise pattern in the evolution of parasitism in the orobanchaceous parasites, and will facilitate future studies on parasitism and the control of parasitic plants in agriculture.

plant biology↗

bioRxiv2018

GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

GetOrganelle is a state-of-the-art toolkit to assemble accurate organelle genomes from NGS data. This toolkit recruit organelle-associated reads using a modified \"baiting and iterative mapping\" approach, conducts de novo assembly, filters and disentangles assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published samples, we reassembled the circular plastome in 47 samples using GetOrganelle, but only in 12 samples using NOVOPlasty. In comparison with published/NOVOPlasty plastomes, we demonstrated that GetOrganelle assemblies are more accurate. Moreover, we assembled complete mitogenomes of fungi and animals using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).

bioinformatics↗