PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts
items: Morphological descriptions and morphometric discriminant function analysis reveal an additional four groups of Scylla spp
items: OLA1 is responsible for normal spindle assembly and SAC activation in mouse oocytes
items: Estimation of regional irrigation water requirements and water balance in Xinjiang, China during 1995–2017
items: Phylogeography of the rare and endangered lycophyte Isoetes yunguiensis
items: The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns
items: Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining
items: Genetic diversity and population structure of two subspecies of western honey bees (Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping
items: Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on communities
items: Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts
type: item
type: AcademicArticle
description: We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated “Edit Plasmids,” were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ re…
format: application/pdf
format: text/html
creator: Byung-Chun Yoo
creator: Narendra S. Yadav
creator: Emil M. Orozco
creator: Hajime Sakai
subject: Bioengineering
subject: Biotechnology
subject: Genetics
subject: Genomics
subject: Synthetic Biology
description: doi:10.7717/peerj.8362
publisher: PeerJ Inc.
rights: © 2020 Yoo et al.
abstract: We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated “Edit Plasmids,” were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ re…
bibliographic citation: Yoo et al. (2020) Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts. PeerJ 8:e8362 https://doi.org/10.7717/peerj.8362
date submitted: 2018-10-16
date accepted: 2019-12-05
issued: 2020-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yoo
  given name: Byung-Chun
author list: Agent
  family name: Yadav
  given name: Narendra S.
author list: Agent
  family name: Orozco
  given name: Emil M.
author list: Agent
  family name: Sakai
  given name: Hajime
doi: 10.7717/peerj.8362
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-06
copyright: © 2020 Yoo et al.
attribution name: Yoo et al.

Morphological descriptions and morphometric discriminant function analysis reveal an additional four groups of Scylla spp
type: item
type: AcademicArticle
description: There are four species of mud crabs within the genus Scylla, and most of them live sympatrically in the equatorial region. Apart from a report in Japan about the finding of a natural Scylla hybrid more than a decade ago after the division of genus Scylla into four species by Keenan, Davie & Mann (1998), no subsequent sighting was found. Thus, this study investigates the possible natural occurrence of potential hybridization among Scylla species in the wild. A total of 76,211 individuals from mud crab landing sites around the Malacca Straits, South China Sea and Sulu Sea were screened. In addition to the four-purebred species, four groups (SH 1, n = 2, 627; SH 2, n = 136; SH 3, n = 1; SH 4, n = 2) with intermediate characteristics were found, mostly at Sulu Sea. Discriminant Function Analysis revealed that all Scylla species, including SH 1 - 4, are distinguishable via their morphometric ratios. The most powerful discriminant ratios for each character and the top five discriminant ratios of males and females were suggested. The carapace width of SH 1 males and females were significantly smaller than pure species. Based on the discriminant ratios and the description of morphological characters, we hypothesize that the additional four groups of Scylla with intermediate characteristics could be presumed hybrids. Future work at the molecular level is urgently needed to validate this postulate.
format: application/pdf
format: text/html
creator: Hanafiah Fazhan
creator: Khor Waiho
creator: Emilia Quinitio
creator: Juliana C. Baylon
creator: Yushinta Fujaya
creator: Nita Rukminasari
creator: Mohammad Farhan Darin Azri
creator: Md. Sheriff Shahreza
creator: Hongyu Ma
creator: Mhd Ikhwanuddin
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
description: doi:10.7717/peerj.8066
publisher: PeerJ Inc.
rights: © 2020 Fazhan et al.
abstract: There are four species of mud crabs within the genus Scylla, and most of them live sympatrically in the equatorial region. Apart from a report in Japan about the finding of a natural Scylla hybrid more than a decade ago after the division of genus Scylla into four species by Keenan, Davie & Mann (1998), no subsequent sighting was found. Thus, this study investigates the possible natural occurrence of potential hybridization among Scylla species in the wild. A total of 76,211 individuals from mud crab landing sites around the Malacca Straits, South China Sea and Sulu Sea were screened. In addition to the four-purebred species, four groups (SH 1, n = 2, 627; SH 2, n = 136; SH 3, n = 1; SH 4, n = 2) with intermediate characteristics were found, mostly at Sulu Sea. Discriminant Function Analysis revealed that all Scylla species, including SH 1 - 4, are distinguishable via their morphometric ratios. The most powerful discriminant ratios for each character and the top five discriminant ratios of males and females were suggested. The carapace width of SH 1 males and females were significantly smaller than pure species. Based on the discriminant ratios and the description of morphological characters, we hypothesize that the additional four groups of Scylla with intermediate characteristics could be presumed hybrids. Future work at the molecular level is urgently needed to validate this postulate.
bibliographic citation: Fazhan et al. (2020) Morphological descriptions and morphometric discriminant function analysis reveal an additional four groups of Scylla spp. PeerJ 8:e8066 https://doi.org/10.7717/peerj.8066
date submitted: 2019-07-05
date accepted: 2019-10-20
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fazhan
  given name: Hanafiah
author list: Agent
  family name: Waiho
  given name: Khor
author list: Agent
  family name: Quinitio
  given name: Emilia
author list: Agent
  family name: Baylon
  given name: Juliana C.
author list: Agent
  family name: Fujaya
  given name: Yushinta
author list: Agent
  family name: Rukminasari
  given name: Nita
author list: Agent
  family name: Azri
  given name: Mohammad Farhan Darin
author list: Agent
  family name: Shahreza
  given name: Md. Sheriff
author list: Agent
  family name: Ma
  given name: Hongyu
author list: Agent
  family name: Ikhwanuddin
  given name: Mhd
doi: 10.7717/peerj.8066
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: ©2020 Fazhan et al.
attribution name: Fazhan et al.

OLA1 is responsible for normal spindle assembly and SAC activation in mouse oocytes
type: item
type: AcademicArticle
description: Background OLA1 is a member of the GTPase protein family; unlike other members, it possess both GTPase and ATPase activities, and can bind and hydrolyze ATP more efficiently than GTP. OLA1 participates in cell proliferation, oxidative response, protein synthesis and tumorigenesis. However, whether OLA1 is also required for oocyte meiosis is still unknown. Methods In this study, the localization, expression, and functions of OLA1 in the mouse oocyte meiosis were examined. Immunofluorescent and confocal microscopy were used to explore the location pattern of OLA1 in the mouse oocyte. Moreover, nocodazole treatment was used to confirm the spindle-like location of OLA1 during mouse meiosis. Western blot was used to explore the expression pattern of OLA1 in the mouse oocyte. Microinjection of siRNA was used to explore the OLA1 functions in the mouse oocyte meiosis. In addition, chromosome spreading was used to investigate the spindle assembly checkpoint (SAC) activity. Results Immunofluorescent staining showed that OLA1 evenly distributed in the cytoplasm at germinal vesicle (GV) stage. After meiosis resumption (GVBD), OLA1 co-localized with spindles, which was further identified by nocodazole treatment experiments. Knockdown of OLA1 impaired the germinal vesicle breakdown progression and finally resulted in a lower polar body extrusion rate. Immunofluorescence analysis indicated that knockdown of OLA1 led to abnormal spindle assembly, which was evidenced by multipolar spindles in OLA1-RNAi-oocytes. After 6 h post-GVBD in culture, an increased proportion of oocyte which has precociously entered into anaphase/telephase I (A/TI) was observed in OLA1-knockdown oocytes, suggesting that loss of OLA1 resulted in the premature segregation of homologous chromosomes. In addition, the chromosome spread analysis suggested that OLA1 knockdown induced premature anaphase onset was due to the precocious inactivation of SAC. Taken together, we concluded that OLA1 plays important role in…
format: application/pdf
format: text/html
creator: Di Xie
creator: Juan Zhang
creator: JinLi Ding
creator: Jing Yang
creator: Yan Zhang
subject: Cell Biology
subject: Developmental Biology
description: doi:10.7717/peerj.8180
publisher: PeerJ Inc.
rights: © 2020 Xie et al.
abstract: Background OLA1 is a member of the GTPase protein family; unlike other members, it possess both GTPase and ATPase activities, and can bind and hydrolyze ATP more efficiently than GTP. OLA1 participates in cell proliferation, oxidative response, protein synthesis and tumorigenesis. However, whether OLA1 is also required for oocyte meiosis is still unknown. Methods In this study, the localization, expression, and functions of OLA1 in the mouse oocyte meiosis were examined. Immunofluorescent and confocal microscopy were used to explore the location pattern of OLA1 in the mouse oocyte. Moreover, nocodazole treatment was used to confirm the spindle-like location of OLA1 during mouse meiosis. Western blot was used to explore the expression pattern of OLA1 in the mouse oocyte. Microinjection of siRNA was used to explore the OLA1 functions in the mouse oocyte meiosis. In addition, chromosome spreading was used to investigate the spindle assembly checkpoint (SAC) activity. Results Immunofluorescent staining showed that OLA1 evenly distributed in the cytoplasm at germinal vesicle (GV) stage. After meiosis resumption (GVBD), OLA1 co-localized with spindles, which was further identified by nocodazole treatment experiments. Knockdown of OLA1 impaired the germinal vesicle breakdown progression and finally resulted in a lower polar body extrusion rate. Immunofluorescence analysis indicated that knockdown of OLA1 led to abnormal spindle assembly, which was evidenced by multipolar spindles in OLA1-RNAi-oocytes. After 6 h post-GVBD in culture, an increased proportion of oocyte which has precociously entered into anaphase/telephase I (A/TI) was observed in OLA1-knockdown oocytes, suggesting that loss of OLA1 resulted in the premature segregation of homologous chromosomes. In addition, the chromosome spread analysis suggested that OLA1 knockdown induced premature anaphase onset was due to the precocious inactivation of SAC. Taken together, we concluded that OLA1 plays important role in…
bibliographic citation: Xie et al. (2020) OLA1 is responsible for normal spindle assembly and SAC activation in mouse oocytes. PeerJ 8:e8180 https://doi.org/10.7717/peerj.8180
date submitted: 2019-06-28
date accepted: 2019-11-08
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Di
author list: Agent
  family name: Zhang
  given name: Juan
author list: Agent
  family name: Ding
  given name: JinLi
author list: Agent
  family name: Yang
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Yan
doi: 10.7717/peerj.8180
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: ©2020 Xie et al.
attribution name: Xie et al.

Estimation of regional irrigation water requirements and water balance in Xinjiang, China during 1995–2017
type: item
type: AcademicArticle
description: Estimating water requirements and water balance for irrigated agricultural areas are important and will facilitate the efficient allocation of water resources for agriculture while minimizing the impact on natural ecosystems in arid regions. Based on the Penman-Monteith formula and GIS technology, the irrigation water requirements (IWR) of three main crops (cotton, corn and wheat) during the growing season were estimated and their spatio-temporal changes over the past 23 years (1995–2017) were analyzed in Xinjiang province, China. Our results indicated a dramatic increase in IWR from 14.12 billion m3 in 1995 to 38.99 billion m3 in 2017 due to the rapid cropland expansion of approximately 2.58 × 104 km2 in this period. Monthly IWR usually peaked in summer from May to July and varied in different basins. From the perspective of crops, cotton was identified to have consumed the largest amount of water, reaching 26.39 billion m3 in 2017, accounting for 67.68% of total water consumption. Spatially, the fastest increasing rate of IWR was Tarim Basin, which was attributable to the increase in water requirement of cotton. By comparing IWR and actual irrigation of Xinjiang in 2014, the amount of water scarcity had reached −15.01 billion m3 (−9.80 billion m3 in Tarim Basin and −6.58 billion m3 in Junggar Basin). The planting areas of three main crops (wheat, corn and cotton) were more sensitive to IWR than rising temperature indicated by our model. This study is of great significance for the scientific allocation of water resources in the irrigated areas of the different prefectures of Xinjiang.
format: application/pdf
format: text/html
creator: Yinbo Li
creator: Hongwei Wang
creator: Yun Chen
creator: Mingjiang Deng
creator: Qian Li
creator: Adiliai Wufu
creator: Dan Wang
creator: Ligang Ma
subject: Natural Resource Management
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.8243
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Estimating water requirements and water balance for irrigated agricultural areas are important and will facilitate the efficient allocation of water resources for agriculture while minimizing the impact on natural ecosystems in arid regions. Based on the Penman-Monteith formula and GIS technology, the irrigation water requirements (IWR) of three main crops (cotton, corn and wheat) during the growing season were estimated and their spatio-temporal changes over the past 23 years (1995–2017) were analyzed in Xinjiang province, China. Our results indicated a dramatic increase in IWR from 14.12 billion m3 in 1995 to 38.99 billion m3 in 2017 due to the rapid cropland expansion of approximately 2.58 × 104 km2 in this period. Monthly IWR usually peaked in summer from May to July and varied in different basins. From the perspective of crops, cotton was identified to have consumed the largest amount of water, reaching 26.39 billion m3 in 2017, accounting for 67.68% of total water consumption. Spatially, the fastest increasing rate of IWR was Tarim Basin, which was attributable to the increase in water requirement of cotton. By comparing IWR and actual irrigation of Xinjiang in 2014, the amount of water scarcity had reached −15.01 billion m3 (−9.80 billion m3 in Tarim Basin and −6.58 billion m3 in Junggar Basin). The planting areas of three main crops (wheat, corn and cotton) were more sensitive to IWR than rising temperature indicated by our model. This study is of great significance for the scientific allocation of water resources in the irrigated areas of the different prefectures of Xinjiang.
bibliographic citation: Li et al. (2020) Estimation of regional irrigation water requirements and water balance in Xinjiang, China during 1995–2017. PeerJ 8:e8243 https://doi.org/10.7717/peerj.8243
date submitted: 2019-07-19
date accepted: 2019-11-19
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yinbo
author list: Agent
  family name: Wang
  given name: Hongwei
author list: Agent
  family name: Chen
  given name: Yun
author list: Agent
  family name: Deng
  given name: Mingjiang
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Wufu
  given name: Adiliai
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Ma
  given name: Ligang
doi: 10.7717/peerj.8243
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: ©2020 Li et al.
attribution name: Li et al.

Phylogeography of the rare and endangered lycophyte Isoetes yunguiensis
type: item
type: AcademicArticle
description: Background Isoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics of I. yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection. Methods Expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure of I. yunguiensis, and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter of I. yunguiensis. A maximum entropy model was used to predict the past, present, and future distribution patterns of I. yunguiensis. Results Analysis with EST-SSR markers revealed that I. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area of I. yunguiensis distribution (NST = 0.344 > GST = 0.183, p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed that I. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area of I. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes.
format: application/pdf
format: text/html
creator: Tao Zheng
creator: Xuanze He
creator: Honghuan Ye
creator: Wei Fu
creator: Maimai Peng
creator: Guangqian Gou
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.8270
publisher: PeerJ Inc.
rights: © 2020 Zheng et al.
abstract: Background Isoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics of I. yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection. Methods Expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure of I. yunguiensis, and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter of I. yunguiensis. A maximum entropy model was used to predict the past, present, and future distribution patterns of I. yunguiensis. Results Analysis with EST-SSR markers revealed that I. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area of I. yunguiensis distribution (NST = 0.344 > GST = 0.183, p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed that I. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area of I. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes.
bibliographic citation: Zheng et al. (2020) Phylogeography of the rare and endangered lycophyte Isoetes yunguiensis. PeerJ 8:e8270 https://doi.org/10.7717/peerj.8270
date submitted: 2019-07-29
date accepted: 2019-11-22
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Tao
author list: Agent
  family name: He
  given name: Xuanze
author list: Agent
  family name: Ye
  given name: Honghuan
author list: Agent
  family name: Fu
  given name: Wei
author list: Agent
  family name: Peng
  given name: Maimai
author list: Agent
  family name: Gou
  given name: Guangqian
doi: 10.7717/peerj.8270
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: ©2020 Zheng et al.
attribution name: Zheng et al.

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns
type: item
type: AcademicArticle
description: Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
format: application/pdf
format: text/html
creator: Sonja I. Repetti
creator: Christopher J. Jackson
creator: Louise M. Judd
creator: Ryan R. Wick
creator: Kathryn E. Holt
creator: Heroen Verbruggen
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.8273
publisher: PeerJ Inc.
rights: © 2020 Repetti et al.
abstract: Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
bibliographic citation: Repetti et al. (2020) The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PeerJ 8:e8273 https://doi.org/10.7717/peerj.8273
date submitted: 2019-10-02
date accepted: 2019-11-22
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Repetti
  given name: Sonja I.
author list: Agent
  family name: Jackson
  given name: Christopher J.
author list: Agent
  family name: Judd
  given name: Louise M.
author list: Agent
  family name: Wick
  given name: Ryan R.
author list: Agent
  family name: Holt
  given name: Kathryn E.
author list: Agent
  family name: Verbruggen
  given name: Heroen
doi: 10.7717/peerj.8273
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: © 2020 Repetti et al.
attribution name: Repetti et al.

Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining
type: item
type: AcademicArticle
description: Background Neurogenic heterotopic ossification is a disorder of aberrant bone formation affecting one in five patients sustaining a spinal cord injury or traumatic brain injury (SCI-TBI-HO). However, the underlying mechanisms of SCI-TBI-HO have proven difficult to elucidate. The aim of the present study is to identify the most promising candidate genes and biological pathways for SCI-TBI-HO. Methods In this study, we used text mining to generate potential explanations for SCI-TBI-HO. Moreover, we employed several additional datasets, including gene expression profile data, drug data and tissue-specific gene expression data, to explore promising genes that associated with SCI-TBI-HO. Results We identified four SCI-TBI-HO-associated genes, including GDF15, LDLR, CCL2, and CLU. Finally, using enrichment analysis, we identified several pathways, including integrin signaling, insulin pathway, internalization of ErbB1, urokinase-type plasminogen activator and uPAR-mediated signaling, PDGFR-beta signaling pathway, EGF receptor (ErbB1) signaling pathway, and class I PI3K signaling events, which may be associated with SCI-TBI-HO. Conclusions These results enhance our understanding of the molecular mechanisms of SCI-TBI-HO and offer new leads for researchers and innovative therapeutic strategies.
format: application/pdf
format: text/html
creator: Yichong Zhang
creator: Yuanbo Zhan
creator: Yuhui Kou
creator: Xiaofeng Yin
creator: Yanhua Wang
creator: Dianying Zhang
subject: Bioinformatics
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.8276
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Neurogenic heterotopic ossification is a disorder of aberrant bone formation affecting one in five patients sustaining a spinal cord injury or traumatic brain injury (SCI-TBI-HO). However, the underlying mechanisms of SCI-TBI-HO have proven difficult to elucidate. The aim of the present study is to identify the most promising candidate genes and biological pathways for SCI-TBI-HO. Methods In this study, we used text mining to generate potential explanations for SCI-TBI-HO. Moreover, we employed several additional datasets, including gene expression profile data, drug data and tissue-specific gene expression data, to explore promising genes that associated with SCI-TBI-HO. Results We identified four SCI-TBI-HO-associated genes, including GDF15, LDLR, CCL2, and CLU. Finally, using enrichment analysis, we identified several pathways, including integrin signaling, insulin pathway, internalization of ErbB1, urokinase-type plasminogen activator and uPAR-mediated signaling, PDGFR-beta signaling pathway, EGF receptor (ErbB1) signaling pathway, and class I PI3K signaling events, which may be associated with SCI-TBI-HO. Conclusions These results enhance our understanding of the molecular mechanisms of SCI-TBI-HO and offer new leads for researchers and innovative therapeutic strategies.
bibliographic citation: Zhang et al. (2020) Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining. PeerJ 8:e8276 https://doi.org/10.7717/peerj.8276
date submitted: 2019-06-29
date accepted: 2019-11-22
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yichong
author list: Agent
  family name: Zhan
  given name: Yuanbo
author list: Agent
  family name: Kou
  given name: Yuhui
author list: Agent
  family name: Yin
  given name: Xiaofeng
author list: Agent
  family name: Wang
  given name: Yanhua
author list: Agent
  family name: Zhang
  given name: Dianying
doi: 10.7717/peerj.8276
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: © 2020 Zhang et al.
attribution name: Zhang et al.

Genetic diversity and population structure of two subspecies of western honey bees (Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping
type: item
type: AcademicArticle
description: Apis mellifera scutellata and Apis mellifera capensis, two native subspecies of western honey bees in the Republic of South Africa (RSA), are important to beekeepers in their native region because beekeepers use these bees for honey production and pollination purposes. Additionally, both bees are important invasive pests outside of their native ranges. Recently, whole mitogenome sequencing and single nucleotide polymorphisms were used to study their genetic diversity. To add to our knowledge of the molecular ecology of both bees, we tested the ability of microsatellites to be used as a tool to discriminate between A.m. capensis and A.m. scutellata. We analyzed the genetic variability and overall population structure of both bee subspecies and hybrids of the two by genotyping individuals collected from RSA (N = 813 bees from 75 apiaries) at 19 microsatellite DNA loci. Overall, populations averaged between 9.2 and 11.3 alleles per locus, with unbiased heterozygosity values ranging from 0.81 to 0.86 per population. Bayesian clustering analyses revealed two distinct evolutionary units, though the results did not match those of earlier morphometric and molecular analyses. This suggests that the microsatellites we tested were not sufficient for subspecies identification purposes, especially for Cape and hybrid bees. Nevertheless, the microsatellite data highlight the considerable genetic diversity within both populations and a larger-than-expected hybridization zone between the natural distributions of A.m. capensis and A.m. scutellata.
format: application/pdf
format: text/html
creator: Amin Eimanifar
creator: Johanna T. Pieplow
creator: Alireza Asem
creator: James D. Ellis
subject: Biodiversity
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.8280
publisher: PeerJ Inc.
rights: © 2020 Eimanifar et al.
abstract: Apis mellifera scutellata and Apis mellifera capensis, two native subspecies of western honey bees in the Republic of South Africa (RSA), are important to beekeepers in their native region because beekeepers use these bees for honey production and pollination purposes. Additionally, both bees are important invasive pests outside of their native ranges. Recently, whole mitogenome sequencing and single nucleotide polymorphisms were used to study their genetic diversity. To add to our knowledge of the molecular ecology of both bees, we tested the ability of microsatellites to be used as a tool to discriminate between A.m. capensis and A.m. scutellata. We analyzed the genetic variability and overall population structure of both bee subspecies and hybrids of the two by genotyping individuals collected from RSA (N = 813 bees from 75 apiaries) at 19 microsatellite DNA loci. Overall, populations averaged between 9.2 and 11.3 alleles per locus, with unbiased heterozygosity values ranging from 0.81 to 0.86 per population. Bayesian clustering analyses revealed two distinct evolutionary units, though the results did not match those of earlier morphometric and molecular analyses. This suggests that the microsatellites we tested were not sufficient for subspecies identification purposes, especially for Cape and hybrid bees. Nevertheless, the microsatellite data highlight the considerable genetic diversity within both populations and a larger-than-expected hybridization zone between the natural distributions of A.m. capensis and A.m. scutellata.
bibliographic citation: Eimanifar et al. (2020) Genetic diversity and population structure of two subspecies of western honey bees (Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping. PeerJ 8:e8280 https://doi.org/10.7717/peerj.8280
date submitted: 2019-10-01
date accepted: 2019-11-22
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eimanifar
  given name: Amin
author list: Agent
  family name: Pieplow
  given name: Johanna T.
author list: Agent
  family name: Asem
  given name: Alireza
author list: Agent
  family name: Ellis
  given name: James D.
doi: 10.7717/peerj.8280
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: © 2020 Eimanifar et al.
attribution name: Eimanifar et al.

Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on communities
type: item
type: AcademicArticle
description: Diatoms are generally regarded as inhabitants of water bodies. However, numerous taxa are able to survive and reproduce in a variety of non-aquatic ecosystems. Although terrestrial diatoms are discussed extensively in the literature, most of those studies covered floristic aspects and few information exists on their ecology. This lack of knowledge thwarts their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal patterns and the role of different disturbances on the community composition. We collected soil diatom samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 14 months. Our results indicate that forests create a stable microhabitat for diatoms and that temporal variation of the diatom communities is mainly controlled by farming practices rather than seasonal changes in environmental variables. We also found out that communities need one to 2 months to reestablish a new, stable community after a significant change in the environment. We were able to confirm the applicability of the Pollution-Sensitivity Index (IPS) to identify anthropic disturbances.
format: application/pdf
format: text/html
creator: Jasper Foets
creator: Carlos E. Wetzel
creator: Adriaan J. Teuling
creator: Laurent Pfister
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Ecohydrology
description: doi:10.7717/peerj.8296
publisher: PeerJ Inc.
rights: © 2020 Foets et al.
abstract: Diatoms are generally regarded as inhabitants of water bodies. However, numerous taxa are able to survive and reproduce in a variety of non-aquatic ecosystems. Although terrestrial diatoms are discussed extensively in the literature, most of those studies covered floristic aspects and few information exists on their ecology. This lack of knowledge thwarts their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal patterns and the role of different disturbances on the community composition. We collected soil diatom samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 14 months. Our results indicate that forests create a stable microhabitat for diatoms and that temporal variation of the diatom communities is mainly controlled by farming practices rather than seasonal changes in environmental variables. We also found out that communities need one to 2 months to reestablish a new, stable community after a significant change in the environment. We were able to confirm the applicability of the Pollution-Sensitivity Index (IPS) to identify anthropic disturbances.
bibliographic citation: Foets et al. (2020) Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on communities. PeerJ 8:e8296 https://doi.org/10.7717/peerj.8296
date submitted: 2019-10-03
date accepted: 2019-11-26
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Foets
  given name: Jasper
author list: Agent
  family name: Wetzel
  given name: Carlos E.
author list: Agent
  family name: Teuling
  given name: Adriaan J.
author list: Agent
  family name: Pfister
  given name: Laurent
doi: 10.7717/peerj.8296
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: © 2020 Foets et al.
attribution name: Foets et al.

Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China
type: item
type: AcademicArticle
description: Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqi…
format: application/pdf
format: text/html
creator: Biao Xiong
creator: Limei Zhang
creator: Shubin Dong
creator: Zhixiang Zhang
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.8304
publisher: PeerJ Inc.
rights: © 2020 Xiong et al.
abstract: Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqi…
bibliographic citation: Xiong et al. (2020) Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China. PeerJ 8:e8304 https://doi.org/10.7717/peerj.8304
date submitted: 2020-03-16
date accepted: 2019-11-27
issued: 2020-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiong
  given name: Biao
author list: Agent
  family name: Zhang
  given name: Limei
author list: Agent
  family name: Dong
  given name: Shubin
author list: Agent
  family name: Zhang
  given name: Zhixiang
doi: 10.7717/peerj.8304
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-03
copyright: ©2020 Xiong et al.
attribution name: Xiong et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359