JianJun Jin

JianJun Jin
Columbia University | CU · Department of Ecology, Evolution and Environmental Biology

PhD

About

32
Publications
16,493
Reads
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1,387
Citations
Introduction
Phylogenetics. Plastome structure evolution.
Additional affiliations
November 2019 - present
Columbia University
Position
  • PostDoc Position
July 2018 - June 2020
Kunming Institute of Botany, Chinese Academy of Sciences
Position
  • Researcher
October 2016 - April 2017
University of Michigan
Position
  • Visiting Student
Education
September 2012 - June 2018
Kunming Institute of Botany, Chinese Academy of Sciences
Field of study
  • Plant phylogenetics
September 2012 - June 2018
Chinese Academy of Sciences
Field of study
  • Plant phylogenetics
September 2008 - July 2012
Jilin University
Field of study
  • Life Science

Publications

Publications (32)
Article
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly...
Preprint
Full-text available
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...
Article
Dispersal scenarios have been favored over tectonic vicariance as an explanation for disjunct distributions in many plant taxa during last two decades. However, this argument has been insufficiently addressed in cosmopolitan groups showing disjunct patterns in both the temperate and tropical regions. In this study, we used the Cannabaceae, an angio...
Article
Full-text available
Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies...
Article
Full-text available
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organell...
Article
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 hol...
Preprint
Full-text available
Orobanchaceae is the largest family of plant parasites comprising autotrophic and parasitic plants with all degrees of parasitism, making 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 holoparasitic...
Article
Full-text available
Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the mos...
Article
Full-text available
Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies...
Article
Full-text available
The typical plastid genome (plastome) of photosynthetic angiosperms comprises a pair of Inverted Repeat regions (IRs), which separate a Large Single Copy region (LSC) from a Small Single Copy region (SSC). The independent losses of IRs have been documented in only a few distinct plant lineages. The majority of these taxa show uncommonly high levels...
Article
Full-text available
The clusioid clade of Malpighiales is comprised of five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae and Podostemaceae. Recent studies have found the plastome structure of Garcinia mangostana L. from Clusiaceae was conserved, while plastomes of five riverweed species from Podostemaceae showed significant structural variations. T...
Article
Full-text available
Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. & C.Fraser, an important medicinal and ornamental...
Article
Full-text available
Klainedoxa gabonensis Pierre ex Engl. is an important tropical tree species. In this study, its complete plastome sequence was determined. This is the first reported complete plastome sequence in the family Irvingiaceae. The plastome is totally 160,118 bp in length, containing a pair of 26,963-bp-long inverted repeat regions (IRs), a large single c...
Article
Full-text available
Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species. To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The I...
Article
Full-text available
The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome) diversification across the subfamily un...
Article
Full-text available
Available plastomes of the Lauraceae show similar structure and varied size, but there has been no systematic comparison across the family. In order to understand the variation in plastome size and structure in the Lauraceae and related families of magnoliids, we here compare 47 plastomes, 15 newly sequenced, from 27 representative genera. We revea...
Article
Full-text available
Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer ste...
Conference Paper
Full-text available
Chloroplast genomes show striking variation in gene content and structure in non-photosynthetic plants. By contrast, hemiparasitic plants have almost complete chloroplast genomes in comparison to their autotrophic relatives. Pedicularis (Orobanchaceae) is a genus of hemiparasitic herbs with over 500 species. In this study, we sequenced total genomi...

Projects

Projects (2)
Project
Carnivorous plants have remarkably similar trap morphologies and attractive features, which have evolved independently across five or six (if including Stylidiaceae of Asterales) orders in angiosperms. These plants can digest and absorb nutrients (especially nitrogen) from their prey, and retain photosynthetic function in general. Analogously, heterotrophic parasitic plants (including root parasites and mycoheterotrophs) steal nutrients from their host plants or fungi; some retain the photosynthetic ability, as in hemiparasites and partial mycoheterotrophs, while some have completely lost photosynthesis, as in holoparasites and holomycotrophs. Investigations of the whole plastid genome have documented pseudogenization or loss of NAD(P)H dehydrogenase (ndh) genes in hemiparasitic plants, as well as genome structural rearrangements, and expansion, contraction, or complete loss of the inverted repeat (IR). A similar scenario is observed in carnivorous plants, but this is based on only a single lineage that has been studied thus far (Lentibulariaceae). In this study, we sequenced 120 species of carnivorous plants, representing six families and five orders of eudicots, using a genome skimming approach. The main goals of this study were to: 1) examine variation in gene content and genome structure across the carnivorous lineages, and 2) investigate molecular evolution of plastid genes in carnivorous lineages in comparison to non-carnivorous sister lineages.
Project
Build the generic-level tree of Fabaceae with chloroplast, mitochondrial and nrDNA data. Reconstruct the evolutionary history of the chloroplast genome structure of Fabaceae.